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As of 1-Apr-2020 number of released structures: 10687
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 7257  Download results as an excel file       Gallery view

NDB ID:

6JPI

PDB ID:

6JPI 

Release:

2020-04-01

Title:

Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa

Classification:

ANTITOXIN/DNA

Authors:

Liu, Y., Gao, Z., Zhang, H., Dong, Y.

Citation:

Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.143Å R work:0.215R free:0.28

NDB ID:

6LFF

PDB ID:

6LFF 

Release:

2020-04-01

Title:

transcription factor SATB1 CUTr1 domain in complex with a phosphorothioate DNA

Classification:

TRANSCRIPTION/DNA

Authors:

Yamasaki, K., Akutsu, Y., Yamasaki, T., Miyagishi, M., Kubota, T.

Citation:

Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.
Nucleic Acids Res. pp. - 2020

Experiment:

X-RAY DIFFRACTION Resolution:1.79Å R work:0.229R free:0.271

NDB ID:

6QWF

PDB ID:

6QWF 

Release:

2020-04-01

Title:

The Transcriptional Regulator PrfA-A94V mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif

Classification:

DNA BINDING PROTEIN

Authors:

Hansen, S., Hall, M., Grundstrom, C., Brannstrom, K., Sauer-Eriksson, A.E., Johansson, J.

Citation:

A novel growth based selection strategy identifies new constitutively active variants of the major virulence regulator PrfA inListeria monocytogenes.
J.Bacteriol. pp. - 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.224R free:0.265

NDB ID:

6QWH

PDB ID:

6QWH 

Release:

2020-04-01

Title:

The Transcriptional Regulator PrfA-L140H mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif

Classification:

DNA BINDING PROTEIN

Authors:

Hansen, S., Hall, M., Grundstrom, C., Brannstrom, K., Sauer-Eriksson, A.E., Johansson, J.

Citation:

A novel growth based selection strategy identifies new constitutively active variants of the major virulence regulator PrfA inListeria monocytogenes.
J.Bacteriol. pp. - 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.254R free:0.291

NDB ID:

6QWK

PDB ID:

6QWK 

Release:

2020-04-01

Title:

The Transcriptional Regulator PrfA-L140F mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif

Classification:

DNA BINDING PROTEIN

Authors:

Hansen, S., Hall, M., Grundstrom, C., Brannstrom, K., Sauer-Eriksson, A.E., Johansson, J.

Citation:

A novel growth based selection strategy identifies new constitutively active variants of the major virulence regulator PrfA inListeria monocytogenes.
J.Bacteriol. pp. - 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.232R free:0.282

NDB ID:

6QWM

PDB ID:

6QWM 

Release:

2020-04-01

Title:

The Transcriptional Regulator PrfA-A218G mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif

Classification:

DNA BINDING PROTEIN

Authors:

Hansen, S., Hall, M., Grundstrom, C., Brannstrom, K., Sauer-Eriksson, A.E., Johansson, J.

Citation:

A novel growth based selection strategy identifies new constitutively active variants of the major virulence regulator PrfA inListeria monocytogenes.
J.Bacteriol. pp. - 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.233R free:0.289

NDB ID:

6R14

PDB ID:

6R14 

Release:

2020-04-01

Title:

Structure of kiteplatinated dsDNA

Classification:

DNA

Authors:

Krejcikova, M., Papadia, P., Gkionis, K., Plats, J., Petruzzella, E., Savino, S., Hoeschelle, J.D., Natile, G., Sponer, J., Kubicek, K., Margiotta, N.

Citation:

Structural characterization of kiteplatinated DNA
To Be Published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

6JOU

PDB ID:

6JOU 

Release:

2020-03-25

Title:

Crystal structure of the human nucleosome containing H2A.Z.1 S42R

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Horikoshi, N., Kusakabe, M., Narimiya, T., Sato, K., Mizukami, Y., Takahashi, D., Kimura, H., Harata, M., Kurumizaka, H.

Citation:

Stability of the nucleosome containing H2A.Z regulates transcription status in cells
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.17Å R work:0.206R free:0.25

NDB ID:

6P5C

PDB ID:

6P5C 

Release:

2020-03-25

Title:

Bacillus Fragment DNA polymerase mutant I716M

Classification:

REPLICATION/DNA

Authors:

Hamm, M.L., Garcia, A.A., Gilbert, R., Johri, M., Ricart, M., Sholes, S.L., Murray-Nerger, L.A., Wu, E.Y.

Citation:

The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase.
DNA Repair (Amst.) 89 pp.102826 - 102826 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.227R free:0.272

NDB ID:

6PCM

PDB ID:

6PCM 

Release:

2020-03-25

Title:

Crystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N- and C-terminal domains

Classification:

ISOMERASE/DNA

Authors:

Tan, K., Cao, N., Tse-Dinh, Y.C.

Citation:

Crystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N- and C-terminal domains.
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.107Å R work:0.225R free:0.275

NDB ID:

6TC8

PDB ID:

6TC8 

Release:

2020-03-25

Title:

2'-F-arabinoguanosine and 2'-F-riboguanosine modified hybrid type G-quadruplex with V-loop

Classification:

DNA

Authors:

Haase, L., Weisz, K.

Citation:

Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions.
Chem.Commun.(Camb.) pp. - 2020

Experiment:

SOLUTION NMR

NDB ID:

6TCG

PDB ID:

6TCG 

Release:

2020-03-25

Title:

2'-F-riboguanosine and 2'-F-arabinoguanosine modified G-quadruplex with V-loop and all-syn G-tract

Classification:

DNA

Authors:

Haase, L., Weisz, K.

Citation:

Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions.
Chem.Commun.(Camb.) pp. - 2020

Experiment:

SOLUTION NMR

NDB ID:

6KN4

PDB ID:

6KN4 

Release:

2020-03-18

Title:

HUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 ADRIAMYCIN (DM2) MOLECULES

Classification:

DNA

Authors:

Barthwal, R., Raje, S., Pandav, K.

Citation:

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4by anticancer drug adriamycin.
J.Biomol.Struct.Dyn. pp.1 - 21 2020

Experiment:

SOLUTION NMR

NDB ID:

6L2N

PDB ID:

6L2N 

Release:

2020-03-18

Title:

Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) complex

Classification:

HYDROLASE/DNA

Authors:

Miyazono, K., Wang, D., Ito, T., Tanokura, M.

Citation:

Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.228R free:0.255

NDB ID:

6L2O

PDB ID:

6L2O 

Release:

2020-03-18

Title:

Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) complex

Classification:

HYDROLASE/DNA

Authors:

Miyazono, K., Wang, D., Ito, T., Tanokura, M.

Citation:

Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.216R free:0.257

NDB ID:

6LDM

PDB ID:

6LDM 

Release:

2020-03-18

Title:

Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Traczyk, A., Liew, C.W., Gill, D.J., Rhodes, D.

Citation:

Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1.
Nucleic Acids Res. pp. - 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.202R free:0.232

NDB ID:

6M3L

PDB ID:

6M3L 

Release:

2020-03-18

Title:

Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex

Classification:

HYDROLASE/DNA

Authors:

Miyazono, K., Wang, D., Ito, T., Tanokura, M.

Citation:

Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.283R free:0.306

NDB ID:

6O8Q

PDB ID:

6O8Q 

Release:

2020-03-18

Title:

HUaa 19bp SYM DNA pH 4.5

Classification:

dna binding protein/dna

Authors:

Remesh, S.G., Hammel, M.

Citation:

HUaa 19bp SYM DNA pH 4.5
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.216Å R work:0.246R free:0.285

NDB ID:

6OAJ

PDB ID:

6OAJ 

Release:

2020-03-18

Title:

HUaE34K 19bp SYM DNA

Classification:

dna binding protein/dna

Authors:

Remesh, S.G., Hammel, M.

Citation:

HUaE34K 19bp SYM DNA
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:4.092Å R work:0.311R free:0.328

NDB ID:

6UR2

PDB ID:

6UR2 

Release:

2020-03-18

Title:

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage

Classification:

REPLICATION/DNA

Authors:

Lelyveld, V.S., Zhang, W., Szostak, J.W.

Citation:

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with DNA template and primer with N3'-> P5' linkage
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.27Å R work:0.229R free:0.276

NDB ID:

6UR4

PDB ID:

6UR4 

Release:

2020-03-18

Title:

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and 3'-amino primer

Classification:

REPLICATION/DNA

Authors:

Lelyveld, V.S., Zhang, W., Szostak, J.W.

Citation:

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with DNA template and 3'-amino primer
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.205R free:0.244

NDB ID:

6UR9

PDB ID:

6UR9 

Release:

2020-03-18

Title:

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+

Classification:

REPLICATION/DNA

Authors:

Lelyveld, V.S., Zhang, W., Szostak, J.W.

Citation:

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.204R free:0.243

NDB ID:

6US5

PDB ID:

6US5 

Release:

2020-03-18

Title:

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+

Classification:

REPLICATION/DNA

Authors:

Lelyveld, V.S., Zhang, W., Szostak, J.W.

Citation:

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.224R free:0.278

NDB ID:

6KON

PDB ID:

6KON 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 5 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.22R free:0.27

NDB ID:

6KOO

PDB ID:

6KOO 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 7 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.206R free:0.247

NDB ID:

6KOP

PDB ID:

6KOP 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 9 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.303Å R work:0.217R free:0.254

NDB ID:

6KOQ

PDB ID:

6KOQ 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 10 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.353Å R work:0.22R free:0.26

NDB ID:

6KQD

PDB ID:

6KQD 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.206R free:0.249

NDB ID:

6KQE

PDB ID:

6KQE 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 4 nt

Classification:

TRANSLATION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.217R free:0.258

NDB ID:

6KQF

PDB ID:

6KQF 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 5 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.198R free:0.229

NDB ID:

6KQG

PDB ID:

6KQG 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 6 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.783Å R work:0.204R free:0.247

NDB ID:

6KQH

PDB ID:

6KQH 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 7 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.18Å R work:0.202R free:0.246

NDB ID:

6KQL

PDB ID:

6KQL 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 4 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.89Å R work:0.207R free:0.246

NDB ID:

6KQM

PDB ID:

6KQM 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 5 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.197Å R work:0.205R free:0.251

NDB ID:

6KQN

PDB ID:

6KQN 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 6 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.489Å R work:0.213R free:0.258

NDB ID:

6L74

PDB ID:

6L74 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 2 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.12Å R work:0.19R free:0.235

NDB ID:

6LTS

PDB ID:

6LTS 

Release:

2020-03-11

Title:

Crystal structure of Thermus thermophilus transcription initiation complex comprising a truncated sigma finger

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.45Å R work:0.22R free:0.258

NDB ID:

6O6K

PDB ID:

6O6K 

Release:

2020-03-11

Title:

HUaa 19bp SYM DNA pH 5.5

Classification:

dna binding protein/dna

Authors:

Remesh, S.G., Hammel, M.

Citation:

HUaa 19bp SYM DNA pH 5.5
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.601Å R work:0.252R free:0.301

NDB ID:

6O6P

PDB ID:

6O6P 

Release:

2020-03-11

Title:

Structure of the regulator FasR from Mycobacterium tuberculosis in complex with DNA

Classification:

TRANSCRIPTION/DNA

Authors:

Lara, J., Trajtenberg, F., Larrieux, N., Gramajo, H., Buschiazzo, A.

Citation:

Crystal structures of FasR uncover the mechanisms of long fatty acyl-CoA sensing and transcriptional activation switching in Mycobacterium tuberculosis
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.851Å R work:0.287R free:0.331

NDB ID:

6TYE

PDB ID:

6TYE 

Release:

2020-03-11

Title:

Crystal structure of MTB sigma L transcription initiation complex with 5 nt long RNA primer

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.79Å R work:0.234R free:0.279

NDB ID:

6TYF

PDB ID:

6TYF 

Release:

2020-03-11

Title:

Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.8Å R work:0.256R free:0.299

NDB ID:

6TYG

PDB ID:

6TYG 

Release:

2020-03-11

Title:

Crystal structure of MTB sigma L transcription initiation complex with 9 nt long RNA primer

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

X-RAY DIFFRACTION Resolution:3.5Å R work:0.246R free:0.293

NDB ID:

6V0L

PDB ID:

6V0L 

Release:

2020-03-11

Title:

PDGFR-b Promoter Forms a G-Vacancy Quadruplex that Can be Complemented by dGMP: Molecular Structure and Recognition of Guanine Derivatives and Metabolites

Classification:

DNA

Authors:

Wang, K.B., Dickerhoff, J., Wu, G., Yang, D.

Citation:

PDGFR-beta Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs.
J.Am.Chem.Soc. 142 pp.5204 - 5211 2020

Experiment:

SOLUTION NMR

NDB ID:

6KDJ

PDB ID:

6KDJ 

Release:

2020-03-04

Title:

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:lamivudine 5'-triphosphate ternary complex

Classification:

TRANSFERASE/DNA

Authors:

Yasutake, Y., Hattori, S.I., Tamura, N., Matsuda, K., Kohgo, S., Maeda, K., Mitsuya, H.

Citation:

Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Sci Rep 10 pp.3021 - 3021 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.51Å R work:0.181R free:0.23

NDB ID:

6KDK

PDB ID:

6KDK 

Release:

2020-03-04

Title:

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex

Classification:

TRANSFERASE/DNA

Authors:

Yasutake, Y., Hattori, S.I., Tamura, N., Matsuda, K., Kohgo, S., Maeda, K., Mitsuya, H.

Citation:

Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Sci Rep 10 pp.3021 - 3021 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.56Å R work:0.189R free:0.234

NDB ID:

6KDM

PDB ID:

6KDM 

Release:

2020-03-04

Title:

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary complex

Classification:

TRANSFERASE/DNA

Authors:

Yasutake, Y., Hattori, S.I., Tamura, N., Matsuda, K., Kohgo, S., Maeda, K., Mitsuya, H.

Citation:

Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Sci Rep 10 pp.3021 - 3021 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.32Å R work:0.189R free:0.222

NDB ID:

6KDN

PDB ID:

6KDN 

Release:

2020-03-04

Title:

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP ternary complex

Classification:

TRANSFERASE/DNA

Authors:

Yasutake, Y., Hattori, S.I., Tamura, N., Matsuda, K., Kohgo, S., Maeda, K., Mitsuya, H.

Citation:

Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Sci Rep 10 pp.3021 - 3021 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.303Å R work:0.186R free:0.221

NDB ID:

6KDO

PDB ID:

6KDO 

Release:

2020-03-04

Title:

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y/M184V/F160M:DNA:lamivudine 5'-triphosphate ternary complex

Classification:

TRANSFERASE/DNA

Authors:

Yasutake, Y., Hattori, S.I., Tamura, N., Matsuda, K., Kohgo, S., Maeda, K., Mitsuya, H.

Citation:

Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Sci Rep 10 pp.3021 - 3021 2020

Experiment:

X-RAY DIFFRACTION Resolution:2.573Å R work:0.191R free:0.23

NDB ID:

6KVB

PDB ID:

6KVB 

Release:

2020-03-04

Title:

Structure of an intra-locked G-quadruplex

Classification:

DNA

Authors:

Maity, A., Winnerdy, F.R., Chang, W.D., Chen, G., Phan, A.T.

Citation:

Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs.
Nucleic Acids Res. pp. - 2020

Experiment:

SOLUTION NMR

NDB ID:

6P7E

PDB ID:

6P7E 

Release:

2020-03-04

Title:

Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase

Classification:

TRANSFERASE/DNA BINDING PROTEIN/DNA

Authors:

Foster, B.M., Rosenberg, D., Salvo, H., Stephens, K.L., Bintz, B.J., Hammel, M., Ellenberger, T., Gainey, M.D., Wallen, J.R.

Citation:

Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.
Biochemistry 58 pp.4466 - 4479 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.001Å R work:0.214R free:0.248