A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 12-Aug-2022 number of released structures: 12231
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4544  Download results as an excel file       Gallery view

NDB ID:

7OOO

PDB ID:

7OOO 

Release:

2022-08-03

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG containing an LNA-Amide-LNA modification

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.57Å R work:0.232R free:0.251

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

7OOS

PDB ID:

7OOS 

Release:

2022-08-03

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.217R free:0.234

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

7OZZ

PDB ID:

7OZZ 

Release:

2022-08-03

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG with LNA-amide modification

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.2R free:0.236

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

7SOP

PDB ID:

7SOP 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAUAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.55Å R work:0.194R free:0.22

Equivalence Class: 

NR_all_62371.1 

Eq. Class Rep:

7SOP

NDB ID:

7SOQ

PDB ID:

7SOQ 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.15Å R work:0.175R free:0.187

Equivalence Class: 

NR_all_65223.6 

Eq. Class Rep:

6Q1H

NDB ID:

7SOR

PDB ID:

7SOR 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.35Å R work:0.18R free:0.204

Equivalence Class: 

NR_all_65223.6 

Eq. Class Rep:

6Q1H

NDB ID:

7SOS

PDB ID:

7SOS 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.25Å R work:0.174R free:0.194

Equivalence Class: 

NR_all_64918.11 

Eq. Class Rep:

7SOS

NDB ID:

7SOT

PDB ID:

7SOT 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAAAA oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.52Å R work:0.19R free:0.211

Equivalence Class: 

NR_all_26685.1 

Eq. Class Rep:

7SOT

NDB ID:

7SOU

PDB ID:

7SOU 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAAAA polynucleotide

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.45Å R work:0.183R free:0.202

Equivalence Class: 

NR_all_77860.1 

Eq. Class Rep:

7SOU

NDB ID:

7SOV

PDB ID:

7SOV 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAAAAAAAAA RNA polynucleotide

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Jiang, J., Mattijssen, S., Gaidamakov, S., Nyandwi, S., Maraia, R., Gehring, K.

Citation:

Structural basis of 3'-end RNA recognition by LARP1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.45Å R work:0.183R free:0.223

Equivalence Class: 

NR_all_42542.1 

Eq. Class Rep:

7SOV

NDB ID:

7QP2

PDB ID:

7QP2 

Release:

2022-07-20

Title:

1-deazaguanosine modified-RNA Sarcin Ricin Loop

Classification:

RNA

Authors:

Bereiter, R., Renard, E., Breuker, K., Kreutz, C., Ennifar, E., Micura, R.

Citation:

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis.
J.Am.Chem.Soc. 144 pp.10344 - 10352 2022

Experiment:

X-RAY DIFFRACTION Resolution:0.9Å R work:0.115R free:0.137

Equivalence Class: 

NR_all_94729.9 

Eq. Class Rep:

4NLF

NDB ID:

7R97

PDB ID:

7R97 

Release:

2022-07-20

Title:

Crystal structure of postcleavge complex of Escherichia coli RNase III

Classification:

HYDROLASE/RNA

Authors:

Dharavath, S., Shaw, G.X., Ji, X.

Citation:

Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg 2+ -ion catalysis.
Rna Biol. 19 pp.908 - 915 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.804Å R work:0.171R free:0.202

Equivalence Class: 

NR_all_52425.2 

Eq. Class Rep:

7R97

NDB ID:

7RWR

PDB ID:

7RWR 

Release:

2022-07-20

Title:

An RNA aptamer that decreases flavin redox potential

Classification:

RNA

Authors:

Gremminger, T., Li, J., Chen, S., Heng, X.

Citation:

An RNA aptamer that increases flavin redox potential
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_89808.1 

Eq. Class Rep:

7RWR

NDB ID:

7UCR

PDB ID:

7UCR 

Release:

2022-07-20

Title:

Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA

Classification:

RNA

Authors:

Harp, J.M., Lybrand, T.P., Pallan, P.S., Coates, L., Sullivan, B., Egli, M.

Citation:

Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure.
Nucleic Acids Res. 50 pp.7721 - 7738 2022

Experiment:

NEUTRON DIFFRACTION Resolution:2.25Å R work:0.254R free:0.298

Equivalence Class: 

NR_all_94729.9 

Eq. Class Rep:

4NLF

NDB ID:

7U2H

PDB ID:

7U2H 

Release:

2022-07-13

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, aminoacylated P-site fMet-NH-tRNAmet, and deacylated E-site tRNAgly at 2.55A resolution

Classification:

RIBOSOME

Authors:

Syroegin, E.A., Aleksandrova, E.V., Polikanov, Y.S.

Citation:

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.
Nucleic Acids Res. 50 pp.7669 - 7679 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.55Å R work:0.219R free:0.262

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

7U2I

PDB ID:

7U2I 

Release:

2022-07-13

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, aminoacylated P-site fMet-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution

Classification:

RIBOSOME

Authors:

Syroegin, E.A., Aleksandrova, E.V., Polikanov, Y.S.

Citation:

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.
Nucleic Acids Res. 50 pp.7669 - 7679 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.55Å R work:0.222R free:0.267

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

7U2J

PDB ID:

7U2J 

Release:

2022-07-13

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, peptidyl P-site fMAC-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution

Classification:

RIBOSOME

Authors:

Syroegin, E.A., Aleksandrova, E.V., Polikanov, Y.S.

Citation:

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.
Nucleic Acids Res. 50 pp.7669 - 7679 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.55Å R work:0.213R free:0.256

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

7F8Z

PDB ID:

7F8Z 

Release:

2022-07-06

Title:

RNA kink-turn motif with 2-aminopurine

Classification:

RNA

Authors:

Kondo, J., Miyauchi, T.

Citation:

RNA kink-turn motif with 2-aminopurine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.175R free:0.228

Equivalence Class: 

NR_all_88157.3 

Eq. Class Rep:

4CS1

NDB ID:

7R8J

PDB ID:

7R8J 

Release:

2022-07-06

Title:

Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA in the presence of Mg2+

Classification:

HYDROLASE/DNA

Authors:

Shin, Y., Murakami, K.S.

Citation:

Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA in the presence of Mg2+
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.205R free:0.244

NDB ID:

7SZU

PDB ID:

7SZU 

Release:

2022-07-06

Title:

Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6

Classification:

IMMUNE SYSTEM/RNA

Authors:

Rees, H.C., Gogacz, W., Li, N.S., Koirala, D., Piccirilli, J.A.

Citation:

Structural Basis for Fluorescence Activation by Pepper RNA.
Acs Chem.Biol. 17 pp.1866 - 1875 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.24Å R work:0.219R free:0.262

Equivalence Class: 

NR_all_02777.1 

Eq. Class Rep:

7SZU

NDB ID:

7UMC

PDB ID:

7UMC 

Release:

2022-07-06

Title:

DENV1 SLA RNA (DenvSLATL)

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Structure of the Dengue Virus RNA Promoter.
Rna pp. - 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_57150.1 

Eq. Class Rep:

7UMC

NDB ID:

7UMD

PDB ID:

7UMD 

Release:

2022-07-06

Title:

DENV1 SLA three-way junction RNA (DenvSLAsh)

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Structure of the Dengue Virus RNA Promoter.
Rna pp. - 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_81668.1 

Eq. Class Rep:

7UMD

NDB ID:

7UME

PDB ID:

7UME 

Release:

2022-07-06

Title:

DENV1 SLA top stemloop RNA (DenvTSL)

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Structure of the Dengue Virus RNA Promoter.
Rna pp. - 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_09835.1 

Eq. Class Rep:

7UME

NDB ID:

7V06

PDB ID:

7V06 

Release:

2022-06-29

Title:

Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for differential binding of hnRNP Splicing Auxiliary Factors

Classification:

RNA

Authors:

Chiu, L.Y., Emery, A., Jain, N., Sugarman, A., Kendrick, N., Luo, L., Ford, W., Swanstrom, R., Tolbert, B.S.

Citation:

Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors.
J.Mol.Biol. pp.167728 - 167728 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_28070.1 

Eq. Class Rep:

7V06

NDB ID:

7F3I

PDB ID:

7F3I 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.184R free:0.245

Equivalence Class: 

NR_all_19366.1 

Eq. Class Rep:

7F3I

NDB ID:

7F3J

PDB ID:

7F3J 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.187R free:0.228

Equivalence Class: 

NR_all_41208.1 

Eq. Class Rep:

7F3J

NDB ID:

7F3K

PDB ID:

7F3K 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.76Å R work:0.145R free:0.175

Equivalence Class: 

NR_all_59550.1 

Eq. Class Rep:

7F3K

NDB ID:

7F3L

PDB ID:

7F3L 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P62

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P62
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.88Å R work:0.194R free:0.231

Equivalence Class: 

NR_all_87638.1 

Eq. Class Rep:

5YTV

NDB ID:

7NRP

PDB ID:

7NRP 

Release:

2022-06-22

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.67Å R work:0.169R free:0.19

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

7UQ6

PDB ID:

7UQ6 

Release:

2022-06-15

Title:

tRNA T-box antiterminator fusion, construct #4

Classification:

RNA

Authors:

Grigg, J.C., Price, I.R., Ke, A.

Citation:

tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-box Riboswitch
to be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.951Å R work:0.246R free:0.264

Equivalence Class: 

NR_all_63075.1 

Eq. Class Rep:

7UQ6

NDB ID:

7VFT

PDB ID:

7VFT 

Release:

2022-06-15

Title:

Crystal structure of rGGGC(CAG)5GUCC oligo

Classification:

RNA

Authors:

An, Y., Chen, Z.S., Chan, H.Y.E., Ngo, J.C.K.

Citation:

Molecular insights into the interaction of CAG trinucleotide RNA repeats with nucleolin and its implication in polyglutamine diseases.
Nucleic Acids Res. 50 pp.7655 - 7668 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.45Å R work:0.195R free:0.207

Equivalence Class: 

NR_all_41768.1 

Eq. Class Rep:

7VFT

NDB ID:

7AZS

PDB ID:

7AZS 

Release:

2022-06-08

Title:

70S thermus thermophilus ribosome with bound antibiotic lead SEQ-569

Classification:

RIBOSOME

Authors:

Zhang, J., Lair, C., Roubert, C., Amaning, K., Barrio, M.B., Benedetti, Y., Cui, Z., Li, X., Baurin, N., Bordon-Pallier, F., Cantalloube, C., Sans, S., Blanc, I., Perron, C., Fraisse, L., Rak, A., Jenner, L.B., Yusupova, G., Yusupov, M., Upton, A., Kaneko, T., Yang, T.J., Fotouhi, N., Nuermberger, E., Tyagi, S., Betoudji, F., Sacchettini, J.C., Lagrange, S.

Citation:

Discovery of natural product derived sequanamycins as potent oral anti-tuberculosis agents
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.246R free:0.274

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

7UZ0

PDB ID:

7UZ0 

Release:

2022-06-08

Title:

AntiT-tRNA flip UCCA

Classification:

RNA

Authors:

Grigg, J.C., Price, I.R., Ke, A.

Citation:

tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-box Riboswitch
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.03Å R work:0.246R free:0.276

Equivalence Class: 

NR_all_91710.1 

Eq. Class Rep:

7UZ0

NDB ID:

7AZO

PDB ID:

7AZO 

Release:

2022-06-01

Title:

70S thermus thermophilus ribosome with bound antibiotic lead SEQ-977

Classification:

RIBOSOME

Authors:

Zhang, J., Lair, C., Roubert, C., Amaning, K., Barrio, M.B., Benedetti, Y., Cui, Z., Li, X., Baurin, N., Bordon-Pallier, F., Cantalloube, C., Sans, S., Blanc, I., Perron, C., Fraisse, L., Rak, A., Jenner, L.B., Yusupova, G., Yusupov, M., Upton, A., Kaneko, T., Yang, T.J., Fotouhi, N., Nuermberger, E., Tyagi, S., Betoudji, F., Sacchettini, J.C., Lagrange, S.

Citation:

Discovery of natural product derived sequanamycins as potent oral anti-tuberculosis agents
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.214R free:0.237

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

7KUB

PDB ID:

7KUB 

Release:

2022-06-01

Title:

Au1 Domain of VEGF Readthrough Element

Classification:

RNA

Authors:

Wagner, N.O., Edwards, J.E., Abramovich, J., Gupta, P., Swaminathan, H., Rouskin, S., D'Souza, V.M.

Citation:

Stop codon readthrough in VEGF-A is regulated by complex signals
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_48437.1 

Eq. Class Rep:

7KUB

NDB ID:

7KUC

PDB ID:

7KUC 

Release:

2022-06-01

Title:

Ax1 Domain of VEGF Readthrough Element

Classification:

RNA

Authors:

Wagner, N.O., Edwards, J.E., Abramovich, J., Gupta, P., Swaminathan, H., Rouskin, S., D'Souza, V.M.

Citation:

Stop codon readthrough in VEGF-A is regulated by complex signals
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_20791.1 

Eq. Class Rep:

7KUC

NDB ID:

7KUD

PDB ID:

7KUD 

Release:

2022-06-01

Title:

Ax2 Domain of VEGF Readthrough Element

Classification:

RNA

Authors:

Wagner, N.O., Edwards, J.E., Abramovich, J., Gupta, P., Swaminathan, H., Rouskin, S., D'Souza, V.M.

Citation:

Stop codon readthrough in VEGF-A is regulated by complex signals
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_70599.1 

Eq. Class Rep:

7KUD

NDB ID:

7P8Q

PDB ID:

7P8Q 

Release:

2022-06-01

Title:

Structure of E.coli RlmJ in complex with an RNA conjugate (GA-SAM)

Classification:

RNA BINDING PROTEIN

Authors:

Meynier, V., Iannazzo, L., Catala, M., Oerum, S., Braud, E., Atdjian, C., Barraud, P., Fonvielle, M., Tisne, C., Etheve-Quelquejeu, M.

Citation:

Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.
Nucleic Acids Res. 50 pp.5793 - 5806 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.289Å R work:0.217R free:0.275

Equivalence Class: 

NR_all_60897.2 

Eq. Class Rep:

6E0O

NDB ID:

7P9I

PDB ID:

7P9I 

Release:

2022-06-01

Title:

Structure of E.coli RlmJ in complex with an RNA conjugate (GAA-SAM)

Classification:

RNA BINDING PROTEIN

Authors:

Meynier, V., Iannazzo, L., Catala, M., Oerum, S., Braud, E., Atdjian, C., Barraud, P., Fonvielle, M., Tisne, C., Etheve-Quelquejeu, M.

Citation:

Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.
Nucleic Acids Res. 50 pp.5793 - 5806 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.594Å R work:0.187R free:0.223

Equivalence Class: 

NR_all_67358.1 

Eq. Class Rep:

7P9I

NDB ID:

7S3A

PDB ID:

7S3A 

Release:

2022-05-25

Title:

Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A.M.K., Cavender, C.E., Tebaldi, T., Jenkins, J.L., Mathews, D.H., Halene, S., Kielkopf, C.L.

Citation:

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
Nucleic Acids Res. 50 pp.5299 - 5312 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.48Å R work:0.13R free:0.157

Equivalence Class: 

NR_all_57351.1 

Eq. Class Rep:

7S3A

NDB ID:

7S3B

PDB ID:

7S3B 

Release:

2022-05-25

Title:

Crystal structure of intact U2AF65 RRM-region bound to AdML-G5 oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A.M.K., Cavender, C.E., Tebaldi, T., Jenkins, J.L., Mathews, D.H., Halene, S., Kielkopf, C.L.

Citation:

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
Nucleic Acids Res. 50 pp.5299 - 5312 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.89Å R work:0.173R free:0.199

Equivalence Class: 

NR_all_57322.1 

Eq. Class Rep:

7S3B

NDB ID:

7S3C

PDB ID:

7S3C 

Release:

2022-05-25

Title:

Crystal structure of intact U2AF65 RRM-region bound to AdML-A5 oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A.M.K., Cavender, C.E., Tebaldi, T., Jenkins, J.L., Mathews, D.H., Halene, S., Kielkopf, C.L.

Citation:

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
Nucleic Acids Res. 50 pp.5299 - 5312 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.51Å R work:0.158R free:0.19

Equivalence Class: 

NR_all_55974.1 

Eq. Class Rep:

7S3C

NDB ID:

7TZR

PDB ID:

7TZR 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch bound to N-methyl-1-(quinoxalin-6-yl)methanamine (compound 16)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.203R free:0.26

Equivalence Class: 

NR_all_42241.3 

Eq. Class Rep:

7TZS

NDB ID:

7TZS

PDB ID:

7TZS 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch in complex with quinoxalin-6-ylmethanamine (compound 17)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.21Å R work:0.204R free:0.244

Equivalence Class: 

NR_all_42241.3 

Eq. Class Rep:

7TZS

NDB ID:

7TZT

PDB ID:

7TZT 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.96Å R work:0.243R free:0.256

Equivalence Class: 

NR_all_42241.3 

Eq. Class Rep:

7TZS

NDB ID:

7TZU

PDB ID:

7TZU 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.87Å R work:0.229R free:0.269

Equivalence Class: 

NR_all_42241.3 

Eq. Class Rep:

7TZS

NDB ID:

7MW8

PDB ID:

7MW8 

Release:

2022-05-18

Title:

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

Classification:

HYDROLASE

Authors:

Carozza, J.A., Cordova, A.F., Brown, J.A., AlSaif, Y., Bohnert, V., Cao, X., Mardjuki, R.E., Skariah, G., Fernandez, D., Li, L.

Citation:

ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling.
Proc.Natl.Acad.Sci.USA 119 pp.e2119189119 - e2119189119 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.242R free:0.303

Equivalence Class: 

NR_all_81965.1 

Eq. Class Rep:

6N6D

NDB ID:

7Z42

PDB ID:

7Z42 

Release:

2022-05-18

Title:

Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B

Classification:

RNA BINDING PROTEIN

Authors:

Krischuns, T., Isel, C., Drncova, P., Lukarska, M., Pflug, A., Paisant, S., Navratil, V., Cusack, S., Naffakh, N.

Citation:

Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD.
Plos Pathog. 18 pp.e1010328 - e1010328 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.418Å R work:0.223R free:0.256

Equivalence Class: 

NR_all_43130.1 

Eq. Class Rep:

7Z42

NDB ID:

7Z43

PDB ID:

7Z43 

Release:

2022-05-11

Title:

Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B

Classification:

RNA BINDING PROTEIN

Authors:

Krischuns, T., Isel, C., Drncova, P., Lukarska, M., Pflug, A., Paisant, S., Navratil, V., Cusack, S., Naffakh, N.

Citation:

Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD.
Plos Pathog. 18 pp.e1010328 - e1010328 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.123Å R work:0.239R free:0.272

Equivalence Class: 

NR_all_45043.4 

Eq. Class Rep:

4WRT

NDB ID:

7Z4O

PDB ID:

7Z4O 

Release:

2022-05-11

Title:

Influenza A/H7N9 polymerase core dimer with Pol II pSer5 CTD peptide mimic bound in site 2A

Classification:

RNA BINDING PROTEIN

Authors:

Krischuns, T., Isel, C., Drncova, P., Lukarska, M., Pflug, A., Paisant, S., Navratil, V., Cusack, S., Naffakh, N.

Citation:

Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD.
Plos Pathog. 18 pp.e1010328 - e1010328 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.412Å R work:0.22R free:0.272

Equivalence Class: 

NR_all_56731.1 

Eq. Class Rep:

7Z4O