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As of 23-Nov-2022 number of released structures: 12471
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4617  Download results as an excel file       Gallery view

NDB ID:

7QA2

PDB ID:

7QA2 

Release:

2022-11-23

Title:

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene

Classification:

RNA

Authors:

Wang, Z., Falk, T., Jurt, S., Johannsen, S., Sigel, R.K.O.

Citation:

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_39772.1 

Eq. Class Rep:

7QA2

NDB ID:

7Z55

PDB ID:

7Z55 

Release:

2022-11-23

Title:

Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrate

Classification:

ANTIVIRAL PROTEIN

Authors:

Molina, R., Garcia-Martin, R., Lopez-Mendez, B., Jensen, A.L.G., Ciges-Tomas, J.R., Marchena-Hurtado, J., Stella, S., Montoya, G.

Citation:

Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases.
Nucleic Acids Res. 50 pp.11199 - 11213 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.664Å R work:0.208R free:0.251

Equivalence Class: 

NR_all_64918.13 

Eq. Class Rep:

7SOS

NDB ID:

8AMG

PDB ID:

8AMG 

Release:

2022-11-23

Title:

Crystal structure of AUGUGGCAU duplex with barium ions (model 1)

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.26Å R work:0.19R free:0.24

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

8AMI

PDB ID:

8AMI 

Release:

2022-11-23

Title:

Crystal structure of AUGUGGCAU duplex with barium ions (model 2)

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.79Å R work:0.182R free:0.236

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

8AMJ

PDB ID:

8AMJ 

Release:

2022-11-23

Title:

Crystal structure of unliganded AUGUGGCAU duplex

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.02Å R work:0.196R free:0.242

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

8AMK

PDB ID:

8AMK 

Release:

2022-11-23

Title:

Crystal structure of AUGUGGCAU duplex crystallized in the presence of calcium ions

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.85Å R work:0.207R free:0.266

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

8AML

PDB ID:

8AML 

Release:

2022-11-23

Title:

Crystal structure of AUGUGGCAU duplex with cadmium ions

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.218R free:0.266

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

8AMM

PDB ID:

8AMM 

Release:

2022-11-23

Title:

Crystal structure of AUGUGGCAU duplex with cesium ions

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.86Å R work:0.221R free:0.268

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

8AMN

PDB ID:

8AMN 

Release:

2022-11-23

Title:

Crystal structure of AUGUGGCAU duplex with strontium ions

Classification:

RNA

Authors:

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

Citation:

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.46Å R work:0.199R free:0.247

Equivalence Class: 

NR_all_15912.1 

Eq. Class Rep:

8AMI

NDB ID:

7Q48

PDB ID:

7Q48 

Release:

2022-11-16

Title:

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8U17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto onco-gene

Classification:

RNA

Authors:

Wang, Z., Jurt, S., Dominguez-Martin, A., Johannsen, S., Sigel, R.K.O.

Citation:

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8U17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto onco-gene
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_16489.1 

Eq. Class Rep:

7Q48

NDB ID:

7Q6L

PDB ID:

7Q6L 

Release:

2022-11-16

Title:

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene

Classification:

RNA

Authors:

Wang, Z., Jurt, S., Dominguez-Martin, A., Johannsen, S., Sigel, R.K.O.

Citation:

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_37077.1 

Eq. Class Rep:

7Q6L

NDB ID:

7W9S

PDB ID:

7W9S 

Release:

2022-11-16

Title:

Crystal structure of the enterovirus 71 polymerase elongation complex (C1S3 form)

Classification:

TRANSFERASE/RNA

Authors:

Li, R., Wang, M., Gong, P.

Citation:

Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis
Nucleic Acids Res. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.53Å R work:0.2R free:0.241

Equivalence Class: 

NR_all_20758.2 

Eq. Class Rep:

5F8J

NDB ID:

8B0R

PDB ID:

8B0R 

Release:

2022-11-16

Title:

Structure of the CalpL/cA4 complex

Classification:

HYDROLASE

Authors:

Rouillon, C., Schneberger, N., Chi, H., Blumenstock, K., Da Vela, S., Ackermann, K., Mocking, J., Peter, M.F., Boenigk, W., Seifert, R., Bode, B.E., Schmid-Burgk, J., Svergun, D., Geyer, M., White, M.F., Hagelueken, G.

Citation:

A tripartite protease triggered type III CRISPR signalling cascade
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.236R free:0.267

Equivalence Class: 

NR_all_64918.13 

Eq. Class Rep:

7SOS

NDB ID:

7MDL

PDB ID:

7MDL 

Release:

2022-11-09

Title:

High-resolution crystal structure of human SepSecS-tRNASec complex

Classification:

TRANSFERASE

Authors:

Puppala, A., French, R.L., Simonovic, M.

Citation:

High-resolution crystal structure of human SepSecS-tRNASec complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.32Å R work:0.175R free:0.202

Equivalence Class: 

NR_all_90840.4 

Eq. Class Rep:

7MDL

NDB ID:

7RGU

PDB ID:

7RGU 

Release:

2022-11-09

Title:

The crystal structure of RocC bound to a transcriptional terminator

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kim, H.J., Edwards, R.A., Glover, J.N.M.

Citation:

The crystal structure of RocC bound to a transcriptional terminator
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.219R free:0.271

Equivalence Class: 

NR_all_19728.1 

Eq. Class Rep:

7RGU

NDB ID:

7SOW

PDB ID:

7SOW 

Release:

2022-11-09

Title:

LaM domain of human LARP1 in complex with UUUUUU

Classification:

RNA BINDING PROTEIN/RNA

Authors:

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

Citation:

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

Experiment:

X-RAY DIFFRACTION Resolution:1.3Å R work:0.182R free:0.192

Equivalence Class: 

NR_all_74924.18 

Eq. Class Rep:

3PEY

NDB ID:

7MKT

PDB ID:

7MKT 

Release:

2022-11-02

Title:

Crystal structure of r(GU)11G-NMM complex

Classification:

RNA

Authors:

Bingman, C.A., Roschdi, S., Nomura, Y., Butcher, S.E.

Citation:

Crystal structure of r(GU)11G-NMM complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.97Å R work:0.268R free:0.291

Equivalence Class: 

NR_all_23264.1 

Eq. Class Rep:

7MKT

NDB ID:

7VSJ

PDB ID:

7VSJ 

Release:

2022-11-02

Title:

Crystal structure of MmIMP3-RRM12 in complex with 9-mer RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Li, X.J., Wu, B.X.

Citation:

Crystal structure of MmIMP3-RRM12 in complex with 9-mer RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.38Å R work:0.203R free:0.261

Equivalence Class: 

NR_all_96910.1 

Eq. Class Rep:

7VSJ

NDB ID:

7VYX

PDB ID:

7VYX 

Release:

2022-11-02

Title:

Crystal structure of the selenomethionine(SeMet)-derived Cas12c1 (D969A) ternary complex

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Zhang, B., Lin, J.Y., Perculija, V., OuYang, S.Y.

Citation:

Crystal structure of the selenomethionine(SeMet)-derived Cas12c1 (D969A) ternary complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.255R free:0.292

Equivalence Class: 

NR_all_31116.1 

Eq. Class Rep:

7VYX

NDB ID:

7QDD

PDB ID:

7QDD 

Release:

2022-10-26

Title:

NMR structure of Npl3 RRM1 bound to the AUCCAA RNA

Classification:

RNA BINDING PROTEIN

Authors:

Moursy, A., Clery, A., Gerhardy, S., Betz, K.M., Rao, S., Campagne, S., Beusch, I., Duszczyk, M.M., Robinson, M.D., Panse, V.G., Allain, F.H.T.

Citation:

The structure of yeast Npl3 bound to RNA reveals a cooperative sequence-specific recognition and an RNA chaperone role in splicing
Biorxiv pp. - 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_63400.1 

Eq. Class Rep:

7QDD

NDB ID:

7QQO

PDB ID:

7QQO 

Release:

2022-10-26

Title:

SpCas9 bound to AAVS1 off-target1 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.212R free:0.246

Equivalence Class: 

NR_all_55025.1 

Eq. Class Rep:

7QQP

NDB ID:

7QQP

PDB ID:

7QQP 

Release:

2022-10-26

Title:

SpCas9 bound to AAVS1 off-target3 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.194R free:0.224

Equivalence Class: 

NR_all_55025.1 

Eq. Class Rep:

7QQP

NDB ID:

7QQQ

PDB ID:

7QQQ 

Release:

2022-10-26

Title:

SpCas9 bound to AAVS1 off-target4 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.65Å R work:0.189R free:0.235

Equivalence Class: 

NR_all_55025.1 

Eq. Class Rep:

7QQP

NDB ID:

7QQR

PDB ID:

7QQR 

Release:

2022-10-26

Title:

SpCas9 bound to AAVS1 off-target5 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.188R free:0.23

Equivalence Class: 

NR_all_55025.1 

Eq. Class Rep:

7QQP

NDB ID:

7QQS

PDB ID:

7QQS 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF on-target DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.197R free:0.228

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QQT

PDB ID:

7QQT 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target1 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.202R free:0.237

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QQU

PDB ID:

7QQU 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target2 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.202R free:0.231

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QQV

PDB ID:

7QQV 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target3 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.194R free:0.23

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QQW

PDB ID:

7QQW 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target4 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.215R free:0.233

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QQX

PDB ID:

7QQX 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target5 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.182R free:0.216

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QQZ

PDB ID:

7QQZ 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target7 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.216R free:0.247

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QR0

PDB ID:

7QR0 

Release:

2022-10-26

Title:

SpCas9 bound to TRAC off-target1 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.193R free:0.223

Equivalence Class: 

NR_all_44791.1 

Eq. Class Rep:

7QR0

NDB ID:

7QR1

PDB ID:

7QR1 

Release:

2022-10-26

Title:

SpCas9 bound to TRAC off-target2 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.206R free:0.23

Equivalence Class: 

NR_all_44791.1 

Eq. Class Rep:

7QR0

NDB ID:

7QR3

PDB ID:

7QR3 

Release:

2022-10-26

Title:

Chimpanzee CPEB3 HDV-like ribozyme

Classification:

RNA

Authors:

Przytula-Mally, A.I., Engilberge, S., Johannsen, S., Olieric, V., Masquida, B., Sigel, R.K.

Citation:

Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes
Biorxiv pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.18Å R work:0.24R free:0.276

Equivalence Class: 

NR_all_82540.1 

Eq. Class Rep:

7QR3

NDB ID:

7QR4

PDB ID:

7QR4 

Release:

2022-10-26

Title:

human CPEB3 HDV-like ribozyme

Classification:

RNA

Authors:

Przytula-Mally, A.I., Engilberge, S., Johannsen, S., Olieric, V., Masquida, B., Sigel, R.K.

Citation:

Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes
Biorxiv pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.83Å R work:0.219R free:0.267

Equivalence Class: 

NR_all_07720.1 

Eq. Class Rep:

7QR4

NDB ID:

7QR5

PDB ID:

7QR5 

Release:

2022-10-26

Title:

SpCas9 bound to FANCF off-target6 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.23R free:0.253

Equivalence Class: 

NR_all_83770.1 

Eq. Class Rep:

7QQX

NDB ID:

7QR7

PDB ID:

7QR7 

Release:

2022-10-26

Title:

SpCas9 bound to AAVS1 off-target2 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.216R free:0.245

Equivalence Class: 

NR_all_55025.1 

Eq. Class Rep:

7QQP

NDB ID:

7QR8

PDB ID:

7QR8 

Release:

2022-10-26

Title:

SpCas9 bound to PTPRC off-target1 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.221R free:0.25

Equivalence Class: 

NR_all_96336.1 

Eq. Class Rep:

7QR8

NDB ID:

7VRL

PDB ID:

7VRL 

Release:

2022-10-26

Title:

Solution structure of Rbfox RRM bound to a non-cognate RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Yang, F., Varani, G.

Citation:

Solution structure of Rbfox RRM bound to a non-cognate RNA
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_91870.1 

Eq. Class Rep:

7VRL

NDB ID:

7ZGV

PDB ID:

7ZGV 

Release:

2022-10-26

Title:

Serratia NucC bound to cA3

Classification:

RNA BINDING PROTEIN

Authors:

Garcia-Doval, C., Mayo-Munoz, D., Smith, L.M., Fineran, P.C.

Citation:

Serratia NucC bound to cA3
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.48Å R work:0.157R free:0.181

Equivalence Class: 

NR_all_65223.7 

Eq. Class Rep:

6Q1H

NDB ID:

7ZO1

PDB ID:

7ZO1 

Release:

2022-10-26

Title:

SpCas9 bound to CD34 off-target9 DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Lin, C.H., Clery, A., Saha, A., Arantes, P.R., Bargsten, K., Irby, M.J., Allain, F.H., Palermo, G., Cameron, P., Donohoue, P.D., Jinek, M.

Citation:

Structural basis for Cas9 off-target activity.
Cell 185 pp.4067 - 4081.e21 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.211R free:0.249

Equivalence Class: 

NR_all_69993.1 

Eq. Class Rep:

7ZO1

NDB ID:

8E0F

PDB ID:

8E0F 

Release:

2022-10-26

Title:

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing a G-G pair adjacent to the target site

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Doherty, E.E., Karki, A., Wilcox, X.E., Mendoza, H.G., Manjunath, A., Matos, V.J., Fisher, A.J., Beal, P.A.

Citation:

ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site.
Nucleic Acids Res. 50 pp.10857 - 10868 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.193R free:0.23

Equivalence Class: 

NR_all_55306.1 

Eq. Class Rep:

8E0F

NDB ID:

8E4X

PDB ID:

8E4X 

Release:

2022-10-26

Title:

Human Adenosine Deaminase Acting on dsRNA (ADAR2-R2D) bound to dsRNA containing a G:3-deaza dA pair adjacent to the target site

Classification:

RNA binding protein/RNA

Authors:

Doherty, E.E., Karki, A., Wilcox, X.E., Mendoza, H.G., Manjunath, A., Matos, V.J., Fisher, A.J., Beal, P.A.

Citation:

ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site.
Nucleic Acids Res. 50 pp.10857 - 10868 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.194R free:0.239

Equivalence Class: 

NR_all_57635.1 

Eq. Class Rep:

8E4X

NDB ID:

7SHX

PDB ID:

7SHX 

Release:

2022-10-19

Title:

A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript, NMR, minimized average structure

Classification:

RNA

Authors:

Sharma, S., Pisignano, G., Merulla, J., Catapano, C.V., Varani, G.

Citation:

A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript.
Nucleic Acids Res. 50 pp.11331 - 11343 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_20520.1 

Eq. Class Rep:

7SHX

NDB ID:

8CVJ

PDB ID:

8CVJ 

Release:

2022-10-19

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution

Classification:

RIBOSOME/RNA

Authors:

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

Citation:

Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.
Nat.Chem. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.246R free:0.294

Equivalence Class: 

NR_all_65795.68 

Eq. Class Rep:

4LFB

NDB ID:

8CVK

PDB ID:

8CVK 

Release:

2022-10-19

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution

Classification:

Ribosome/RNA

Authors:

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

Citation:

Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.
Nat.Chem. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.235R free:0.284

Equivalence Class: 

NR_all_65795.68 

Eq. Class Rep:

4LFB

NDB ID:

8CVL

PDB ID:

8CVL 

Release:

2022-10-19

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMTHSMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.30A resolution

Classification:

Ribosome/RNA

Authors:

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

Citation:

Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.
Nat.Chem. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.237R free:0.281

Equivalence Class: 

NR_all_65795.68 

Eq. Class Rep:

4LFB

NDB ID:

7VKI

PDB ID:

7VKI 

Release:

2022-10-05

Title:

ESRP1 qRRM2 in complex with 12mer-RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Wu, B.X., Patel, D.J.

Citation:

ESRP1 qRRM2 in complex with 12mer-RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.65Å R work:0.194R free:0.22

Equivalence Class: 

NR_all_32759.1 

Eq. Class Rep:

7VKI

NDB ID:

7VKL

PDB ID:

7VKL 

Release:

2022-10-05

Title:

Crystal structure of MmIMP3-KH12 in complex with zipcode RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Li, X.J., Wu, B.X.

Citation:

Crystal structure of MmIMP3-KH12 in complex with zipcode RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.212R free:0.256

Equivalence Class: 

NR_all_18395.1 

Eq. Class Rep:

7VKL

NDB ID:

7XPL

PDB ID:

7XPL 

Release:

2022-10-05

Title:

Crystal structure of a C/D-free RNA-guided RNA 2'-O-methyltransferase

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Wang, J., Yang, Z., Ye, K.

Citation:

Methylation guide RNAs without box C/D motifs.
Rna pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.213Å R work:0.188R free:0.236

Equivalence Class: 

NR_all_64498.1 

Eq. Class Rep:

7XPL