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As of 26-Jul-2017 number of released structures: 9000
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 6073  Download results as an excel file       Gallery view

NDB ID:

5GKR

PDB ID:

5GKR 

Release:

2017-07-05

Title:

Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide

Classification:

IMMUNE SYSTEM/DNA

Authors:

Sakakibara, S., Arimori, T., Yamashita, K., Jinzai, H., Motooka, D., Nakamura, S., Li, S., Takeda, K., Yasui, T., Narazaki, M., Tanaka, T., Standley, D.M., Takagi, J., Kikutani, H.

Citation:

Clonal evolution and antigen-recognition of anti-nuclear antibodies in acute systemic lupus erythematosus
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.162R free:0.185

NDB ID:

5IX7

PDB ID:

5IX7 

Release:

2017-07-05

Title:

Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array

Classification:

DNA

Authors:

Kondo, J., Tada, Y., Dairaku, T., Hattori, Y., Saneyoshi, H., Ono, A., Tanaka, Y.

Citation:

A metallo-DNA nanowire with uninterrupted one-dimensional silver array
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.398Å R work:0.165R free:0.188

NDB ID:

5TWP

PDB ID:

5TWP 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.001Å R work:0.185R free:0.237

NDB ID:

5TWQ

PDB ID:

5TWQ 

Release:

2017-07-05

Title:

Post-catalytic nicked complex of human Polymerase Mu with newly incorporated UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.167R free:0.204

NDB ID:

5TWR

PDB ID:

5TWR 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu (H329A) mutant with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.162R free:0.194

NDB ID:

5TWS

PDB ID:

5TWS 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (H329A) with newly incorporated UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.85Å R work:0.166R free:0.2

NDB ID:

5VZ7

PDB ID:

5VZ7 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu (G433A) mutant with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.551Å R work:0.17R free:0.187

NDB ID:

5VZ8

PDB ID:

5VZ8 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (G433A) mutant with incoming UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.601Å R work:0.171R free:0.193

NDB ID:

5VZ9

PDB ID:

5VZ9 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (G433A) mutant with incoming dTTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.65Å R work:0.16R free:0.19

NDB ID:

5VZA

PDB ID:

5VZA 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu (G433S) mutant with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.501Å R work:0.168R free:0.183

NDB ID:

5VZB

PDB ID:

5VZB 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (G433S) mutant with incoming UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.17R free:0.187

NDB ID:

5VZC

PDB ID:

5VZC 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (G433S) mutant with incoming dTTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.552Å R work:0.165R free:0.19

NDB ID:

5VZD

PDB ID:

5VZD 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu (W434A) mutant with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.602Å R work:0.165R free:0.182

NDB ID:

5VZE

PDB ID:

5VZE 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (W434A) mutant with incoming UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.506Å R work:0.177R free:0.2

NDB ID:

5VZF

PDB ID:

5VZF 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (W434A) mutant with incoming dTTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.65Å R work:0.169R free:0.195

NDB ID:

5VZG

PDB ID:

5VZG 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu (W434H) mutant with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.85Å R work:0.175R free:0.201

NDB ID:

5VZH

PDB ID:

5VZH 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.178R free:0.21

NDB ID:

5VZI

PDB ID:

5VZI 

Release:

2017-07-05

Title:

Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming dTTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.171R free:0.193

NDB ID:

5X21

PDB ID:

5X21 

Release:

2017-07-05

Title:

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM)

Classification:

TRANSFERASE/DNA

Authors:

Maffioli, S.I., Zhang, Y., Degen, D., Carzaniga, T., Del Gatto, G., Serina, S., Monciardini, P., Mazzetti, C., Guglierame, P., Candiani, G., Chiriac, A.I., Facchetti, G., Kaltofen, P., Sahl, H.G., Deho, G., Donadio, S., Ebright, R.H.

Citation:

Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.
Cell 169 pp.1240 - 1248.e23 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.323Å R work:0.231R free:0.28

NDB ID:

5X22

PDB ID:

5X22 

Release:

2017-07-05

Title:

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and CMPcPP

Classification:

TRANSFERASE/DNA

Authors:

Maffioli, S.I., Zhang, Y., Degen, D., Carzaniga, T., Del Gatto, G., Serina, S., Monciardini, P., Mazzetti, C., Guglierame, P., Candiani, G., Chiriac, A.I., Facchetti, G., Kaltofen, P., Sahl, H.G., Deho, G., Donadio, S., Ebright, R.H.

Citation:

Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.
Cell 169 pp.1240 - 1248.e23 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.35Å R work:0.207R free:0.25

NDB ID:

5GTC

PDB ID:

5GTC 

Release:

2017-06-28

Title:

Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle

Classification:

STRUCTURAL PROTEIN/DNA

Authors:

Amamoto, Y., Aoi, Y., Nagashima, N., Suto, H., Yoshidome, D., Arimura, Y., Osakabe, A., Kato, D., Kurumizaka, H., Kawashima, S.A., Yamatsugu, K., Kanai, M.

Citation:

Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.
J. Am. Chem. Soc. 139 pp.7568 - 7576 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.211R free:0.266

NDB ID:

5K97

PDB ID:

5K97 

Release:

2017-06-28

Title:

Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+

Classification:

HYDROLASE/DNA

Authors:

Tsutakawa, S.E., Arvai, A.S., Thompson, M.J., Finger, L.D., Rashid, F., Neil, A., Kim, J.C., Sarker, A.S., Mirkin, S.M., Hamdan, S.M., Grasby, J.A., Tainer, J.A.

Citation:

Flap endonuclease 1 D233N with cleaved product fragment
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.102Å R work:0.182R free:0.218

NDB ID:

5KSE

PDB ID:

5KSE 

Release:

2017-06-28

Title:

Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and Sm3+

Classification:

HYDROLASE/DNA

Authors:

Tsutakawa, S.E., Thompson, M.J., Arvai, A.S., Finger, L.D., Rashid, F., Neil, A., Kim, J.C., Sarker, A.S., Hamdan, S.M., Mirkin, S.M., Grasby, J.A., Tainer, J.A.

Citation:

Flap Endonuclease 1 R100A and substrate DNA?
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.105Å R work:0.207R free:0.245

NDB ID:

5NIP

PDB ID:

5NIP 

Release:

2017-06-28

Title:

An i-motif containing the neutral cytidine protonated analogue pseudoisocytidine

Classification:

DNA

Authors:

Mir, B., Soles, X., Gonzalez, C., Escaja, N.

Citation:

The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures.
Sci Rep 7 pp.2772 - 2772 2017

Experiment:

SOLUTION NMR

NDB ID:

5NJ8

PDB ID:

5NJ8 

Release:

2017-06-28

Title:

Structural basis for aryl hydrocarbon receptor mediated gene activation

Classification:

TRANSCRIPTION

Authors:

Schulte, K.W., Green, E., Wilz, A., Platten, M., Daumke, O.

Citation:

Structural Basis for Aryl Hydrocarbon Receptor-Mediated Gene Activation.
Structure pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.292R free:0.332

NDB ID:

5NKL

PDB ID:

5NKL 

Release:

2017-06-28

Title:

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP

Classification:

TRANSFERASE

Authors:

Betz, K., Kimoto, M., Diederichs, K., Hirao, I., Marx, A.

Citation:

Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair.
Angew. Chem. Int. Ed. Engl. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.7Å R work:0.18R free:0.236

NDB ID:

5TRN

PDB ID:

5TRN 

Release:

2017-06-28

Title:

Solution Structure of a DNA Dodecamer with 8-oxoguanine at the 4th position and 5-methylcytosine at the 9th position

Classification:

DNA

Authors:

Hoppins, J.J., Gruber, D.R., Miears, H.L., Endutkin, A.V., Zharkov, D.O., Smirnov, S.L.

Citation:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 4th position
To Be Published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

5UM9

PDB ID:

5UM9 

Release:

2017-06-28

Title:

Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+

Classification:

Hydrolase/DNA

Authors:

Tsutakawa, S.E., Arvai, A.S., Tainer, J.A.

Citation:

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability
NAT COMMUN pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.805Å R work:0.207R free:0.265

NDB ID:

5VC8

PDB ID:

5VC8 

Release:

2017-06-28

Title:

Crystal structure of the WHSC1 PWWP1 domain

Classification:

DNA BINDING PROTEIN

Authors:

Qin, S., Tempel, W., Dong, A., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J.

Citation:

Crystal structure of the WHSC1 PWWP1 domain
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.199R free:0.228

NDB ID:

5VC9

PDB ID:

5VC9 

Release:

2017-06-28

Title:

Zinc finger of human CXXC4 in complex with CpG DNA

Classification:

DNA BINDING PROTEIN

Authors:

Liu, K., Xu, C., Tempel, W., Walker, J.R., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J.

Citation:

Zinc finger of human CXXC4 in complex with CpG DNA
to be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.21R free:0.248

NDB ID:

5W7N

PDB ID:

5W7N 

Release:

2017-06-28

Title:

2-Se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

Classification:

HYDROLASE/DNA/RNA

Authors:

Fang, Z., Yang, F., Huang, Z.

Citation:

2-Se-T2/4-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.192R free:0.232

NDB ID:

5W7O

PDB ID:

5W7O 

Release:

2017-06-28

Title:

2-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

Classification:

HYDROLASE/DNA/RNA

Authors:

Fang, Z., Yang, F., Huang, Z.

Citation:

2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.75Å R work:0.182R free:0.228

NDB ID:

5IU5

PDB ID:

5IU5 

Release:

2017-06-21

Title:

Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCICCGA)2

Classification:

DNA

Authors:

Keane, P.M., Hall, J.P., Poynton, F.E., Gurung, S.P., Clark, I.P., Sazanovich, I.V., Towrie, M., Gunnlaugsson, T., Brazier, J.A., Quinn, S.J., Cardin, C.J., Kelly, J.M.

Citation:

Unexpected enhancement of sensitised photo-oxidation by a Ru(II) complex on replacement of guanine with inosine in DNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.198R free:0.209

NDB ID:

5J70

PDB ID:

5J70 

Release:

2017-06-21

Title:

The Chd1 DNA-binding domain in complex with 17mer DNA duplex

Classification:

chromatin-binding protein/DNA

Authors:

Nodelman, I.M., Jenkins, K.R., Ren, R., Horvath, K.C., Hauk, G., Bowman, G.D.

Citation:

Chd1 domains communicate across the DNA gyres of the nucleosome
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.956Å R work:0.23R free:0.251

NDB ID:

5MGA

PDB ID:

5MGA 

Release:

2017-06-21

Title:

Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage

Classification:

HYDROLASE

Authors:

Stella, S., Alcon, P., Montoya, G.

Citation:

Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage.
Nature 546 pp.559 - 563 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.241R free:0.265

NDB ID:

5TJG

PDB ID:

5TJG 

Release:

2017-06-21

Title:

Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp

Classification:

Transferase/DNA

Authors:

Feklistov, A., Bae, B., Hauver, J., Lass-Napiorkowska, A., Kalesse, M., Glaus, F., Altmann, K.H., Heyduk, T., Landick, R., Darst, S.A.

Citation:

RNA polymerase motions during promoter melting.
Science 356 pp.863 - 866 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.224R free:0.261

NDB ID:

5XEW

PDB ID:

5XEW 

Release:

2017-06-21

Title:

Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex

Classification:

DNA/ANTIBIOTIC

Authors:

Tseng, W.H., Chang, C.K., Wu, P.C., Hu, N.J., Lee, G.H., Tzeng, C.C., Neidle, S., Hou, M.H.

Citation:

Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation
Angew. Chem. Int. Ed. Engl. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.751Å R work:0.207R free:0.237

NDB ID:

5J4P

PDB ID:

5J4P 

Release:

2017-06-14

Title:

DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium

Classification:

DNA

Authors:

Dvorkin, S.A., Webba da Silva, M.

Citation:

DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium
To Be Published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

5LIT

PDB ID:

5LIT 

Release:

2017-06-14

Title:

Structure of the DNA duplex d(AAATTT)2 with the potential antiparasitic drug 6XV at 1.25 A resolution

Classification:

DNA

Authors:

Millan, C.R., Acosta-Reyes, F.J., Lagartera, L., Ebiloma, G.U., Lemgruber, L., Nue Martinez, J.J., Saperas, N., Dardonville, C., de Koning, H.P., Campos, J.L.

Citation:

Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast.
Nucleic Acids Res. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:1.25Å R work:0.12R free:0.166

NDB ID:

5N9G

PDB ID:

5N9G 

Release:

2017-06-14

Title:

TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-

Classification:

TRANSCRIPTION

Authors:

Gouge, J., Vannini, A., Guthertz, N.

Citation:

Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA Polymerase III transcription initiation
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.194R free:0.233

NDB ID:

5NFV

PDB ID:

5NFV 

Release:

2017-06-14

Title:

Crystal structure of catalytically inactive FnCas12 mutant bound to an R-loop structure containing a pre-crRNA mimic and full-length DNA target

Classification:

HYDROLASE

Authors:

Swarts, D.C., van der Oost, J., Jinek, M.

Citation:

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.
Mol. Cell 66 pp.221 - 233.e4 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.501Å R work:0.205R free:0.237

NDB ID:

5NW5

PDB ID:

5NW5 

Release:

2017-06-14

Title:

Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA

Classification:

DNA BINDING PROTEIN

Authors:

Mattarocci, S., Reinert, J.K., Bunker, R.D., Fontana, G.A., Shi, T., Klein, D., Cavadini, S., Faty, M., Shyian, M., Hafner, L., Shore, D., Thoma, N.H., Rass, U.

Citation:

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends.
Nat. Struct. Mol. Biol. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:6.502Å R work:0.252R free:0.276

NDB ID:

5XH6

PDB ID:

5XH6 

Release:

2017-06-14

Title:

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Nishimasu, H., Yamano, T., Gao, L., Zhang, F., Ishitani, R., Nureki, O.

Citation:

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1
Mol.Cell 67 pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.174R free:0.209

NDB ID:

5XH7

PDB ID:

5XH7 

Release:

2017-06-14

Title:

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR variant in complex with crRNA and target DNA (TCCA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Nishimasu, H., Yamano, T., Gao, L., Zhang, F., Ishitani, R., Nureki, O.

Citation:

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1
Mol.Cell 67 pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.182R free:0.214

NDB ID:

5LTY

PDB ID:

5LTY 

Release:

2017-05-31

Title:

Homeobox transcription factor CDX2 bound to methylated DNA

Classification:

TRANSCRIPTION

Authors:

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F., Nitta, K.R., Taipale, M., Popov, A., Ginno, P.A., Domcke, S., Yan, J., Schubeler, D., Vinson, C., Taipale, J.

Citation:

Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Science 356 pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.66Å R work:0.202R free:0.242

NDB ID:

5M1L

PDB ID:

5M1L 

Release:

2017-05-31

Title:

Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

Classification:

DNA

Authors:

Kocman, V., Plavec, J.

Citation:

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Nat Commun 8 pp.15355 - 15355 2017

Experiment:

SOLUTION NMR

NDB ID:

5M2L

PDB ID:

5M2L 

Release:

2017-05-31

Title:

Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

Classification:

DNA

Authors:

Kocman, V., Plavec, J.

Citation:

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Nat Commun 8 pp.15355 - 15355 2017

Experiment:

SOLUTION NMR

NDB ID:

5M4W

PDB ID:

5M4W 

Release:

2017-05-31

Title:

Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleotide found in regulatory region of the PLEKHG3 human gene with G11 to I11 mutation, d(GCGAGGGAGCIAGGG),VK34_I11

Classification:

DNA

Authors:

Kocman, V., Plavec, J.

Citation:

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Nat Commun 8 pp.15355 - 15355 2017

Experiment:

SOLUTION NMR

NDB ID:

5MVB

PDB ID:

5MVB 

Release:

2017-05-31

Title:

Solution structure of a human G-Quadruplex hybrid-2 form in complex with a Gold-ligand

Classification:

DNA

Authors:

Wirmer-Bartoschek, J., Bendel, L.E., Jonker, H.R.A., Grun, J.T., Papi, F., Bazzicalupi, C., Messori, L., Gratteri, P., Schwalbe, H.

Citation:

Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.
Angew. Chem. Int. Ed. Engl. 56 pp.7102 - 7106 2017

Experiment:

SOLUTION NMR

NDB ID:

5UZ1

PDB ID:

5UZ1 

Release:

2017-05-31

Title:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd position and 8-oxoguanine at the 10th position

Classification:

DNA

Authors:

Gruber, D.R., Hoppins, J.J., Miears, H.L., Endutkin, A.V., Zharkov, D.O., Smirnov, S.L.

Citation:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd position 8-oxoguanine at the 10th position
To Be Published pp. - 0

Experiment:

SOLUTION NMR