A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 18-Sep-2019 number of released structures: 10387
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 7039  Download results as an excel file       Gallery view

NDB ID:

 6H3R

PDB ID:

6H3R 

Release:

2019-09-18

Title:

Crystal structure of Smad2 without exon -MH1 bound to the CAGAC site.

Classification:

TRANSCRIPTION

Authors:

Ruiz, L., Kaczmarska, Z., Aragon, E., Gomes, T., Martin Malpartida, P., de Martin Garrido, N., Freier, R., Marquez, J.A., Macias, M.J.

Citation:

Recognition of 5GC DNA motifs is conserved in BMP and TGF-beta activated Smads
to be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.75Å R work:0.201R free:0.222

NDB ID:

 6GN2

PDB ID:

6GN2 

Release:

2019-09-11

Title:

Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group R3

Classification:

DNA

Authors:

Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.

Citation:

Racemic crystal structures of A-DNA duplexes
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.48Å R work:0.258R free:0.272

NDB ID:

 6GN3

PDB ID:

6GN3 

Release:

2019-09-11

Title:

Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group P21/n

Classification:

DNA

Authors:

Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.

Citation:

Racemic crystal structures of A-DNA duplexes
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.279R free:0.318

NDB ID:

 6IDO

PDB ID:

6IDO 

Release:

2019-09-11

Title:

Crystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA

Classification:

TRANSCRIPTION

Authors:

Lou, Y.C., Chou, C.C., Yeh, H.H., Chien, C.Y., Sadotra, S., Hsu, C.H., Chen, C.

Citation:

Constructing well-folded sigma4 domains from bacterial sigma70 and sigmaS factors for -35 element DNA recognition and transcription factor interaction
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.748Å R work:0.222R free:0.252

NDB ID:

 6KI6

PDB ID:

6KI6 

Release:

2019-09-11

Title:

Crystal structure of BCL11A in complex with gamma-globin -115 HPFH region

Classification:

TRANSCRIPTION/DNA

Authors:

Yang, Y., Xu, Z., He, C., Zhang, B., Shi, Y., Li, F.

Citation:

Structural insights into the recognition of gamma-globin gene promoter by BCL11A.
Cell Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.206R free:0.251

NDB ID:

 6OZF

PDB ID:

6OZF 

Release:

2019-09-04

Title:

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.8Å R work:0.166R free:0.197

NDB ID:

 6OZG

PDB ID:

6OZG 

Release:

2019-09-04

Title:

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.93Å R work:0.177R free:0.209

NDB ID:

 6OZH

PDB ID:

6OZH 

Release:

2019-09-04

Title:

Crystal structure of Ciona intestinalis (Ci) Endonuclease V in complex with a 24mer DNA containing an inosine followed by a ribo-adenosine

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.026Å R work:0.233R free:0.269

NDB ID:

 6OZI

PDB ID:

6OZI 

Release:

2019-09-04

Title:

Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.302Å R work:0.174R free:0.201

NDB ID:

 6OZJ

PDB ID:

6OZJ 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine in the absence of divalent cation

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.247Å R work:0.156R free:0.193

NDB ID:

 6OZK

PDB ID:

6OZK 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after 68h soak in Ca2+

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.104Å R work:0.176R free:0.214

NDB ID:

 6OZL

PDB ID:

6OZL 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 2 min soak in Mn2+

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.175R free:0.216

NDB ID:

 6OZM

PDB ID:

6OZM 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 10 min soak in 10 mM Mn2+

Classification:

HYDROLASE/RNA

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.15Å R work:0.173R free:0.216

NDB ID:

 6OZN

PDB ID:

6OZN 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mn2+

Classification:

HYDROLASE/RNA

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.191R free:0.221

NDB ID:

 6OZO

PDB ID:

6OZO 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 30 min soak in 10 mM Mn2+

Classification:

HYDROLASE/RNA

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.235Å R work:0.168R free:0.211

NDB ID:

 6OZP

PDB ID:

6OZP 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+

Classification:

HYDROLASE/RNA

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.96Å R work:0.174R free:0.201

NDB ID:

 6OZQ

PDB ID:

6OZQ 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V (K155M) in complex with a 23mer RNA oligo containing an inosine after a 100 min soak in 10 mM Mn2+ and K+

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.153Å R work:0.173R free:0.209

NDB ID:

 6OZR

PDB ID:

6OZR 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mg2+

Classification:

HYDROLASE

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.15Å R work:0.157R free:0.194

NDB ID:

 6OZS

PDB ID:

6OZS 

Release:

2019-09-04

Title:

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mM Mg2+

Classification:

HYDROLASE/RNA

Authors:

Wu, J., Samara, N.L., Kuraoka, I., Yang, W.

Citation:

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.41Å R work:0.19R free:0.236

NDB ID:

 6P1M

PDB ID:

6P1M 

Release:

2019-09-04

Title:

Binary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.65Å R work:0.165R free:0.189

NDB ID:

 6P1N

PDB ID:

6P1N 

Release:

2019-09-04

Title:

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dAMPNPP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.6Å R work:0.165R free:0.186

NDB ID:

 6P1O

PDB ID:

6P1O 

Release:

2019-09-04

Title:

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dAMP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.65Å R work:0.167R free:0.187

NDB ID:

 6P1P

PDB ID:

6P1P 

Release:

2019-09-04

Title:

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dCMPNPP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.75Å R work:0.164R free:0.184

NDB ID:

 6P1Q

PDB ID:

6P1Q 

Release:

2019-09-04

Title:

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dCMP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.168R free:0.206

NDB ID:

 6P1R

PDB ID:

6P1R 

Release:

2019-09-04

Title:

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming AMPNPP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.701Å R work:0.174R free:0.194

NDB ID:

 6P1S

PDB ID:

6P1S 

Release:

2019-09-04

Title:

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated AMP

Classification:

TRANSFERASE/DNA

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.75Å R work:0.172R free:0.195

NDB ID:

 6P1T

PDB ID:

6P1T 

Release:

2019-09-04

Title:

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound CMPCPP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.7Å R work:0.169R free:0.19

NDB ID:

 6P1U

PDB ID:

6P1U 

Release:

2019-09-04

Title:

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated CMP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.75Å R work:0.169R free:0.192

NDB ID:

 6P1V

PDB ID:

6P1V 

Release:

2019-09-04

Title:

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing undamaged template dG and bound incoming dCMPNPP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.95Å R work:0.176R free:0.203

NDB ID:

 6P1W

PDB ID:

6P1W 

Release:

2019-09-04

Title:

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing undamaged template dG and bound incoming CMPCPP

Classification:

TRANSFERASE

Authors:

Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Nucleic Acids Res. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.751Å R work:0.163R free:0.189

NDB ID:

 6IS7

PDB ID:

6IS7 

Release:

2019-08-28

Title:

Structure of 9N-I DNA polymerase incorporation with dA in the active site

Classification:

TRANSFERASE/DNA

Authors:

LinWu, S.W., Tu, Y.H., Tsai, T.Y., Maestre-Reyna, M., Liu, M.S., Wu, W.J., Huang, J.Y., Chi, H.W., Chang, W.H., Chiou, C.F., Wang, A.H., Lee, J., Tsai, M.D.

Citation:

Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol 2 pp.224 - 224 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.224R free:0.276

NDB ID:

 6ISF

PDB ID:

6ISF 

Release:

2019-08-28

Title:

Structure of 9N-I DNA polymerase incorporation with dT in the active site

Classification:

TRANSFERASE/DNA

Authors:

LinWu, S.W., Tu, Y.H., Tsai, T.Y., Maestre-Reyna, M., Liu, M.S., Wu, W.J., Huang, J.Y., Chi, H.W., Chang, W.H., Chiou, C.F., Wang, A.H., Lee, J., Tsai, M.D.

Citation:

Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol 2 pp.224 - 224 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.231R free:0.271

NDB ID:

 6ISG

PDB ID:

6ISG 

Release:

2019-08-28

Title:

Structure of 9N-I DNA polymerase incorporation with dG in the active site

Classification:

TRANSFERASE/DNA

Authors:

LinWu, S.W., Tu, Y.H., Tsai, T.Y., Maestre-Reyna, M., Liu, M.S., Wu, W.J., Huang, J.Y., Chi, H.W., Chang, W.H., Chiou, C.F., Wang, A.H., Lee, J., Tsai, M.D.

Citation:

Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol 2 pp.224 - 224 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.401Å R work:0.252R free:0.301

NDB ID:

 6ISH

PDB ID:

6ISH 

Release:

2019-08-28

Title:

Structure of 9N-I DNA polymerase incorporation with 3'-AL in the active site

Classification:

TRANSFERASE/DNA

Authors:

LinWu, S.W., Tu, Y.H., Tsai, T.Y., Maestre-Reyna, M., Liu, M.S., Wu, W.J., Huang, J.Y., Chi, H.W., Chang, W.H., Chiou, C.F., Wang, A.H., Lee, J., Tsai, M.D.

Citation:

Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol 2 pp.224 - 224 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.3Å R work:0.215R free:0.278

NDB ID:

 6ISI

PDB ID:

6ISI 

Release:

2019-08-28

Title:

Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site

Classification:

TRANSFERASE/DNA

Authors:

LinWu, S.W., Tu, Y.H., Tsai, T.Y., Maestre-Reyna, M., Liu, M.S., Wu, W.J., Huang, J.Y., Chi, H.W., Chang, W.H., Chiou, C.F., Wang, A.H., Lee, J., Tsai, M.D.

Citation:

Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol 2 pp.224 - 224 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.2Å R work:0.231R free:0.29

NDB ID:

 6J7Y

PDB ID:

6J7Y 

Release:

2019-08-28

Title:

Human mitochondrial Oligoribonuclease in complex with DNA

Classification:

HYDROLASE

Authors:

Chu, L.Y., Agrawal, S., Chen, Y.P., Yang, W.Z., Yuan, H.S.

Citation:

Structural insights into nanoRNA degradation by human Rexo2.
Rna 25 pp.737 - 746 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.203Å R work:0.198R free:0.243

NDB ID:

 6J80

PDB ID:

6J80 

Release:

2019-08-28

Title:

Human mitochondrial Oligoribonuclease in complex with poly-dT DNA

Classification:

HYDROLASE/DNA

Authors:

Chu, L.Y., Agrawal, S., Chen, Y.P., Yang, W.Z., Yuan, H.S.

Citation:

Structural insights into nanoRNA degradation by human Rexo2.
Rna 25 pp.737 - 746 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.812Å R work:0.193R free:0.212

NDB ID:

 6JCD

PDB ID:

6JCD 

Release:

2019-08-28

Title:

G-quadruplex peripheral knot

Classification:

DNA

Authors:

Truong, T.H.A., Winnerdy, F.R., Phan, A.T.

Citation:

An Unprecedented Knot-like G-Quadruplex Peripheral Motif.
Angew.Chem.Int.Ed.Engl. pp. - 2019

Experiment:

 SOLUTION NMR

NDB ID:

 6JR4

PDB ID:

6JR4 

Release:

2019-08-28

Title:

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster

Classification:

DNA

Authors:

Cerretani, C., Kanazawa, H., Vosch, T., Kondo, J.

Citation:

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster.
Angew.Chem.Int.Ed.Engl. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.798Å R work:0.126R free:0.145

NDB ID:

 6PW2

PDB ID:

6PW2 

Release:

2019-08-28

Title:

Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication

Classification:

viral protein/dna

Authors:

Malecka, K.A., Dheekollu, J., Deakyne, J.S., Wiedmer, A., Ramirez, U.D., Lieberman, P.M., Messick, T.E.

Citation:

Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication.
J. Virol. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.01Å R work:0.219R free:0.277

NDB ID:

 6Q0C

PDB ID:

6Q0C 

Release:

2019-08-28

Title:

MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with undamaged dG

Classification:

hydrolase/DNA

Authors:

Russelburg, L.P., O'Shea Murray, V.L., Demir, M., Knutsen, K.R., Sehgal, S.L., Cao, S., David, S.S., Horvath, M.P.

Citation:

Structural basis for finding OG lesions and avoiding undamaged G by the DNA glycosylase MutY
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.247R free:0.27

NDB ID:

 6RNL

PDB ID:

6RNL 

Release:

2019-08-28

Title:

L-[Ru(TAP)2(dppz)]2+ bound to the G-quadruplex forming sequence d(TAGGGTT)

Classification:

DNA

Authors:

McQuaid, K., Hall, J.P., Baumgaertner, L., Cardin, D.J., Cardin, C.J.

Citation:

Three thymine/adenine binding modes of the ruthenium complex Lambda-[Ru(TAP)2(dppz)]2+to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography.
Chem.Commun.(Camb.) 55 pp.9116 - 9119 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.88Å R work:0.187R free:0.214

NDB ID:

 6DG0

PDB ID:

6DG0 

Release:

2019-08-21

Title:

MEC-8 C-terminal RRM domain bound to AGCACA

Classification:

RNA BINDING PROTEIN/DNA

Authors:

Soufari, H., Mackereth, C.D.

Citation:

Structure of MEC-8 RRM2 in complex with AGCACA
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.457Å R work:0.234R free:0.287

NDB ID:

 6Q2B

PDB ID:

6Q2B 

Release:

2019-08-21

Title:

Crystal Structure of Putative MarR Family Transcriptional Regulator from Listeria monocytogenes complexed with 26mer DNA

Classification:

TRANSCRIPTION

Authors:

Kim, Y., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Citation:

Crystal Structure of Putative MarR Family Transcriptional Regulator from Listeria monocytogenes complexed with 26mer DNA.
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.72Å R work:0.232R free:0.251

NDB ID:

 6ED9

PDB ID:

6ED9 

Release:

2019-08-14

Title:

NMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGA)

Classification:

DNA

Authors:

Davis, E.V., Hennig, M., Arya, D.P.

Citation:

An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 6PY8

PDB ID:

6PY8 

Release:

2019-08-14

Title:

Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Jarrett, S.M., Seegar, T.C.M., Andrews, M., Adelmant, G., Marto, J.A., Aster, J.C., Blacklow, S.C.

Citation:

Molecular basis for feedback inhibition of Notch signaling by the Notch regulated ankyrin repeat protein NRARP
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.75Å R work:0.266R free:0.314

NDB ID:

 6KIJ

PDB ID:

6KIJ 

Release:

2019-08-07

Title:

Crystal structure of yedK with ssDNA containing an abasic site

Classification:

DNA BINDING PROTEIN

Authors:

Wang, N., Bao, H., Huang, H.

Citation:

Crystal structure of yedK
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.58Å R work:0.151R free:0.182

NDB ID:

 6H0S

PDB ID:

6H0S 

Release:

2019-07-31

Title:

Crystal structure of the complex between the Lactococcus lactis FPG mutant G226P and a Fapy-dG containing DNA

Classification:

HYDROLASE

Authors:

Coste, F., Castaing, B., Carell, T.

Citation:

Crystal structure of the complex between the Lactococcus lactis FPG mutant G226P and a Fapy-dG containing DNA
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.75Å R work:0.156R free:0.177

NDB ID:

 6IOD

PDB ID:

6IOD 

Release:

2019-07-31

Title:

The structure of UdgX in complex with single-stranded DNA

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Tu, J., Chen, R., Yang, Y., Cao, W., Xie, W.

Citation:

Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.
Nat.Chem.Biol. 15 pp.615 - 622 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.66Å R work:0.182R free:0.216

NDB ID:

 6JRP

PDB ID:

6JRP 

Release:

2019-07-31

Title:

Crystal structure of CIC-HMG-ETV5-DNA complex

Classification:

TRANSCRIPTION

Authors:

Lee, H., Song, J.J.

Citation:

The crystal structure of Capicua HMG-box domain complexed with the ETV5-DNA and its implications for Capicua-mediated cancers.
Febs J. pp. - 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.296R free:0.334

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