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As of 18-Jul-2018 number of released structures: 9608
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 6491  Download results as an excel file       Gallery view

NDB ID:

5W6K

PDB ID:

5W6K 

Release:

2018-07-18

Title:

Structure of mutant Taq Polymerase incorporating unnatural base pairs Z:P

Classification:

DNA binding protein/DNA

Authors:

Singh, I., Laos, R., Hoshika, S., Benner, S.A., Georgiadis, M.M.

Citation:

Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.
Nucleic Acids Res. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.339Å R work:0.224R free:0.274

NDB ID:

5W6Q

PDB ID:

5W6Q 

Release:

2018-07-18

Title:

Structural basis for recognition of artificial DNA by an evolved KlenTaq variant

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Singh, I., Laos, R., Hoshika, S., Benner, S.A., Georgiadis, M.M.

Citation:

Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.
Nucleic Acids Res. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.66Å R work:0.211R free:0.247

NDB ID:

5Y0C

PDB ID:

5Y0C 

Release:

2018-07-18

Title:

Crystal Structure of the human nucleosome at 2.09 angstrom resolution

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H.

Citation:

Cancer-associated mutations of histones H2B, H3.1, and H2A.Z.1 affect the structure and stability of the nucleosome
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.087Å R work:0.201R free:0.249

NDB ID:

5Y0D

PDB ID:

5Y0D 

Release:

2018-07-18

Title:

Crystal Structure of the human nucleosome containing the H2B E76K mutant

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H.

Citation:

Cancer-associated mutations of histones H2B, H3.1, and H2A.Z.1 affect the structure and stability of the nucleosome
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.99Å R work:0.21R free:0.252

NDB ID:

5Z30

PDB ID:

5Z30 

Release:

2018-07-18

Title:

The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H.

Citation:

Cancer-associated mutations of histones H2B, H3.1, and H2A.Z.1 affect the structure and stability of the nucleosome
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.201R free:0.243

NDB ID:

6BKF

PDB ID:

6BKF 

Release:

2018-07-18

Title:

Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation

Classification:

LIGASE/DNA

Authors:

Kaminski, A.M., Tumbale, P.P., Schellenberg, M.J., Williams, R.S., Williams, J.G., Kunkel, T.A., Pedersen, L.C., Bebenek, K.

Citation:

Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.
Nat Commun 9 pp.2642 - 2642 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.25Å R work:0.263R free:0.315

NDB ID:

6BKG

PDB ID:

6BKG 

Release:

2018-07-18

Title:

Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation

Classification:

LIGASE/DNA

Authors:

Kaminski, A.M., Tumbale, P.P., Schellenberg, M.J., Williams, R.S., Williams, J.G., Kunkel, T.A., Pedersen, L.C., Bebenek, K.

Citation:

Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.
Nat Commun 9 pp.2642 - 2642 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.402Å R work:0.201R free:0.245

NDB ID:

6BUX

PDB ID:

6BUX 

Release:

2018-07-18

Title:

CRYSTAL STRUCTURE OF APOBEC3G CATALYTIC DOMAIN COMPLEX WITH SUBSTRATE SSDNA

Classification:

HYDROLASE/DNA

Authors:

Maiti, A., Myint, W., Kanai, T., Delviks-Frankenberry, K., Sierra Rodriguez, C., Pathak, V.K., Schiffer, C.A., Matsuo, H.

Citation:

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA.
Nat Commun 9 pp.2460 - 2460 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.856Å R work:0.178R free:0.211

NDB ID:

6CR4

PDB ID:

6CR4 

Release:

2018-07-18

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dATP

Classification:

TRANSFERASE/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.172R free:0.213

NDB ID:

6CR5

PDB ID:

6CR5 

Release:

2018-07-18

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2-beta, gamma dATP analogue

Classification:

TRANSFERASE/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.982Å R work:0.177R free:0.231

NDB ID:

6CRB

PDB ID:

6CRB 

Release:

2018-07-18

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dATP analogue

Classification:

TRANSFERASE/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.151Å R work:0.217R free:0.274

NDB ID:

6CT9

PDB ID:

6CT9 

Release:

2018-07-18

Title:

Structure of the human cGAS-DNA complex

Classification:

TRANSFERASE/DNA

Authors:

Zhou, W., Whiteley, A.T., de Oliveira Mann, C.C., Morehouse, B.R., Mekalanos, J.J., Kranzusch, P.J.

Citation:

Structure of the human cGAS-DNA complex reveals enhanced control of immune surveillance
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.26Å R work:0.199R free:0.228

NDB ID:

6CTA

PDB ID:

6CTA 

Release:

2018-07-18

Title:

Structure of the human cGAS-DNA complex with ATP

Classification:

TRANSFERASE/DNA

Authors:

Zhou, W., Whiteley, A.T., de Oliveira Mann, C.C., Morehouse, B.R., Mekalanos, J.J., Kranzusch, P.J.

Citation:

Structure of the human cGAS-DNA complex reveals enhanced control of immune surveillance
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.779Å R work:0.21R free:0.245

NDB ID:

6FB0

PDB ID:

6FB0 

Release:

2018-07-18

Title:

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Calcium

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.15Å R work:0.176R free:0.229

NDB ID:

6FB1

PDB ID:

6FB1 

Release:

2018-07-18

Title:

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Magnesium

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.024Å R work:0.208R free:0.251

NDB ID:

6FB2

PDB ID:

6FB2 

Release:

2018-07-18

Title:

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Manganese

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.95Å R work:0.186R free:0.234

NDB ID:

6FB5

PDB ID:

6FB5 

Release:

2018-07-18

Title:

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Magnesium

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.188R free:0.219

NDB ID:

6FB6

PDB ID:

6FB6 

Release:

2018-07-18

Title:

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Manganese

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.192R free:0.242

NDB ID:

6FB7

PDB ID:

6FB7 

Release:

2018-07-18

Title:

Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with its target DNA in the presence of Manganese

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.689Å R work:0.163R free:0.211

NDB ID:

6FB8

PDB ID:

6FB8 

Release:

2018-07-18

Title:

Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of Magnesium

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.186R free:0.223

NDB ID:

6FB9

PDB ID:

6FB9 

Release:

2018-07-18

Title:

Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of Manganese

Classification:

DNA BINDING PROTEIN

Authors:

Prieto, J., Redondo, P., Lopez-Mendez, B., D'Abramo, M., Merino, N., Blanco, F.J., Duchateau, P., Montoya, G., Molina, R.

Citation:

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Sci Rep 8 pp.10286 - 10286 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.95Å R work:0.167R free:0.203

NDB ID:

6DT7

PDB ID:

6DT7 

Release:

2018-07-11

Title:

Bacteriophage N4 RNA polymerase II and DNA complex

Classification:

transcription/dna

Authors:

Molodtsov, V., Murakami, K.S.

Citation:

Bacteriophage N4 RNA polymerase II and DNA complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.189R free:0.214

NDB ID:

6DT8

PDB ID:

6DT8 

Release:

2018-07-11

Title:

Bacteriophage N4 RNA polymerase II elongation complex 1

Classification:

transcription/dna/rna

Authors:

Molodtsov, V., Murakami, K.S.

Citation:

Bacteriophage N4 RNA polymerase II elongation complex 1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.189R free:0.242

NDB ID:

6DTA

PDB ID:

6DTA 

Release:

2018-07-11

Title:

Bacteriophage N4 RNA polymerase II elongation complex 2

Classification:

transcription/dna/rna

Authors:

Molodtsov, V., Murakami, K.S.

Citation:

Bacteriophage N4 RNA polymerase II elongation complex 2
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.694Å R work:0.19R free:0.222

NDB ID:

6C31

PDB ID:

6C31 

Release:

2018-07-04

Title:

Crystal structure of TetR family protein Rv0078 in complex with DNA

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Samanovic, M.I., Hsu, H.C., Jones, M.B., Jones, V., McNeil, M.R., Becker, S.H., Jordan, A.T., Strnad, M., Xu, C., Jackson, M., Li, H., Darwin, K.H.

Citation:

Cytokinin Signaling in Mycobacterium tuberculosis.
MBio 9 pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.201R free:0.246

NDB ID:

6CR7

PDB ID:

6CR7 

Release:

2018-07-04

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF, beta, gamma dATP analogue

Classification:

TRANSFERASE/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.29Å R work:0.173R free:0.24

NDB ID:

6CR8

PDB ID:

6CR8 

Release:

2018-07-04

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers), beta, gamma dATP analogue

Classification:

TRANSFERASE/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.05Å R work:0.19R free:0.248

NDB ID:

6CR9

PDB ID:

6CR9 

Release:

2018-07-04

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dATP analogue

Classification:

TRANSFERASE/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.96Å R work:0.179R free:0.223

NDB ID:

6CVP

PDB ID:

6CVP 

Release:

2018-07-04

Title:

Human Aprataxin (Aptx) R199H bound to RNA-DNA, AMP and Zn product complex

Classification:

HYDROLASE/DNA/RNA

Authors:

Tumbale, P., Schellenberg, M.J., Mueller, G.A., Fairweather, E., Watson, M., Little, J.N., Krahn, J., Waddell, I., London, R.E., Williams, R.S.

Citation:

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
EMBO J. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.999Å R work:0.164R free:0.213

NDB ID:

6CVQ

PDB ID:

6CVQ 

Release:

2018-07-04

Title:

Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex

Classification:

HYDROLASE/DNA/RNA

Authors:

Tumbale, P., Schellenberg, M.J., Mueller, G.A., Fairweather, E., Watson, M., Little, J.N., Krahn, J., Waddell, I., London, R.E., Williams, R.S.

Citation:

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
EMBO J. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.65Å R work:0.117R free:0.167

NDB ID:

6CVR

PDB ID:

6CVR 

Release:

2018-07-04

Title:

Human Aprataxin (Aptx) S242N bound to RNA-DNA, AMP and Zn product complex

Classification:

HYDROLASE/DNA/RNA

Authors:

Tumbale, P., Schellenberg, M.J., Mueller, G.A., Fairweather, E., Watson, M., Little, J.N., Krahn, J., Waddell, I., London, R.E., Williams, R.S.

Citation:

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
EMBO J. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.88Å R work:0.166R free:0.189

NDB ID:

6CVS

PDB ID:

6CVS 

Release:

2018-07-04

Title:

Human Aprataxin (Aptx) L248M bound to DNA, AMP and Zn product

Classification:

hydrolase/dna

Authors:

Tumbale, P., Schellenberg, M.J., Mueller, G.A., Fairweather, E., Watson, M., Little, J.N., Krahn, J., Waddell, I., London, R.E., Williams, R.S.

Citation:

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
EMBO J. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.11Å R work:0.173R free:0.196

NDB ID:

6CVT

PDB ID:

6CVT 

Release:

2018-07-04

Title:

Human Aprataxin (Aptx) V263G bound to RNA-DNA, AMP and Zn product complex

Classification:

HYDROLASE/DNA/RNA

Authors:

Tumbale, P., Schellenberg, M.J., Mueller, G.A., Fairweather, E., Watson, M., Little, J.N., Krahn, J., Waddell, I., London, R.E., Williams, R.S.

Citation:

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
EMBO J. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.941Å R work:0.246R free:0.289

NDB ID:

6G2Q

PDB ID:

6G2Q 

Release:

2018-07-04

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (S-isomer), beta, gamma dTTP analogue

Classification:

REPLICATION

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.148Å R work:0.195R free:0.259

NDB ID:

5OR5

PDB ID:

5OR5 

Release:

2018-06-27

Title:

NMR structure of the complex formed by an engineered region 2 of sigmaE in complex with GTAAAA

Classification:

TRANSCRIPTION

Authors:

Campagne, S., Vorholt, J.A., Allain, F.H.

Citation:

Engineered promoter selectivity of an ECF sigma factor
To be published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

5VL9

PDB ID:

5VL9 

Release:

2018-06-27

Title:

Crystal structure of EilR in complex with eilO DNA element

Classification:

TRANSCRIPTION/DNA

Authors:

Ruegg, T.L., Pereira, J.H., Chen, J., Novichkov, P., DeGiovani, A., Tomaleri, G.P., Singer, S., Simmons, B., Adams, P.D., Thelen, M.

Citation:

A multispecific repressor for precise transcriptional control
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.16Å R work:0.194R free:0.228

NDB ID:

5W6W

PDB ID:

5W6W 

Release:

2018-06-27

Title:

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

Classification:

DNA

Authors:

Hernandez, C., Birktoft, J.J., Seeman, N.C., Ohayon, Y.P., Chandrasekaran, A.R., Abdalla, H.O., Mohsen, M., Sha, R., Chenge, M., Lukeman, P.S., Chaikin, P., Ginell, S.L., Jong, M.A.

Citation:

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.06Å R work:0.223R free:0.24

NDB ID:

6CR3

PDB ID:

6CR3 

Release:

2018-06-27

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue

Classification:

transcription/DNA

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.174R free:0.226

NDB ID:

6FJ5

PDB ID:

6FJ5 

Release:

2018-06-27

Title:

p53-DNA complex 5

Classification:

TRANSCRIPTION

Authors:

Golovenko, D., Rozenberg, H., Shakked, Z.

Citation:

p53-DNA complex 5
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.051Å R work:0.198R free:0.243

NDB ID:

5ORQ

PDB ID:

5ORQ 

Release:

2018-06-20

Title:

Crystal structure of designed cPPR-Telo1 in complex with ssDNA

Classification:

DE NOVO PROTEIN

Authors:

Spahr, H., Chia, T., Lingford, J.P., Siira, S.J., Cohen, S.B., Filipovska, A., Rackham, O.

Citation:

Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.
Nat Commun 9 pp.2212 - 2212 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.188R free:0.228

NDB ID:

5W4U

PDB ID:

5W4U 

Release:

2018-06-20

Title:

Pol II elongation complex with an N6-methyladenine-containing template

Classification:

DNA BINDING PROTEIN/RNA/DNA

Authors:

Wang, W., Wang, D.

Citation:

Pol II elongation complex with an N6-methyladenine-containing template
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.226R free:0.259

NDB ID:

5W51

PDB ID:

5W51 

Release:

2018-06-20

Title:

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP

Classification:

DNA BINDING PROTEIN/RNA/DNA

Authors:

Wang, W., Wang, D.

Citation:

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.404Å R work:0.226R free:0.253

NDB ID:

5XSK

PDB ID:

5XSK 

Release:

2018-06-20

Title:

Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor

Classification:

HORMONE

Authors:

Chen, L.Y., Huang, Y.C., Hsieh, Y.C., Lin, P.J.

Citation:

Structure of PWWP-DNA complex at 2.84 Angstroms resolution
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.84Å R work:0.191R free:0.269

NDB ID:

5ZK1

PDB ID:

5ZK1 

Release:

2018-06-20

Title:

Crystal Structure of the CRTC2(SeMet)-CREB-CRE complex

Classification:

TRANSCRIPTION/DNA

Authors:

Song, Y., Zhai, L., Valencia Swain, J., Chen, Y., Wang, P., Chen, L., Liu, Y., Xiang, S.

Citation:

Structural Insights into the CRTC2-CREB Complex Assembly on CRE.
J. Mol. Biol. 430 pp.1926 - 1939 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.228R free:0.268

NDB ID:

5ZKO

PDB ID:

5ZKO 

Release:

2018-06-20

Title:

Crystal structure of the CRTC2-CREB-CRE complex

Classification:

TRANSCRIPTION/DNA

Authors:

Song, Y., Zhai, L., Valencia Swain, J., Chen, Y., Wang, P., Chen, L., Liu, Y., Xiang, S.

Citation:

Structural Insights into the CRTC2-CREB Complex Assembly on CRE.
J. Mol. Biol. 430 pp.1926 - 1939 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.242R free:0.284

NDB ID:

6CCW

PDB ID:

6CCW 

Release:

2018-06-20

Title:

Hybrid-2 form Human Telomeric G Quadruplex in Complex with Epiberberine

Classification:

DNA

Authors:

Lin, C., Wu, G., Wang, K., Onel, B., Sakai, S., Shao, Y., Yang, D.

Citation:

Molecular Recognition of the Hybrid-2 Human Telomeric G-quadruplex by Epiberberine: Insights into Conversion of Telomeric G-quadruplex Structures.
Angew. Chem. Int. Ed. Engl. pp. - 2018

Experiment:

SOLUTION NMR

NDB ID:

6CTI

PDB ID:

6CTI 

Release:

2018-06-20

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dTTP analogue

Classification:

transcription/dna

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.001Å R work:0.176R free:0.226

NDB ID:

6CTJ

PDB ID:

6CTJ 

Release:

2018-06-20

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCH3, beta, gamma dTTP analogue

Classification:

transcription/dna

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.19R free:0.257

NDB ID:

6CTK

PDB ID:

6CTK 

Release:

2018-06-20

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF-R/S isomers, beta, gamma dTTP analogue

Classification:

transcription/dna

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.153Å R work:0.178R free:0.244

NDB ID:

6CTL

PDB ID:

6CTL 

Release:

2018-06-20

Title:

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL-R/S isomers, beta, gamma dTTP analogue

Classification:

Transcription/dna

Authors:

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Citation:

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Biochemistry 57 pp.3934 - 3944 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.179R free:0.225