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As of 21-Sep-2022 number of released structures: 12282
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4561  Download results as an excel file       Gallery view

NDB ID:

 7XS4

PDB ID:

7XS4 

Release:

2022-09-21

Title:

Crystal structure of URT1 in complex with AAAU RNA

Classification:

PLANT PROTEIN/RNA

Authors:

Hu, Q., Zhu, L.R.

Citation:

Molecular Mechanism Underlying the Di-uridylation Activity of Arabidopsis TUTase URT1
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.846Å R work:0.173R free:0.201

Equivalence Class: 

NR_all_24351.1 

Eq. Class Rep:

7XS4

NDB ID:

 7PMM

PDB ID:

7PMM 

Release:

2022-09-14

Title:

DEAD-box helicase DbpA in the active conformation bound to a ss/dsRNA junction and ADP/BeF3

Classification:

RNA BINDING PROTEIN

Authors:

Wurm, J.P.

Citation:

DEAD-box helicase DbpA bound to a ss/dsRNA junction and ADP/BeF3
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.197R free:0.224

Equivalence Class: 

NR_all_74379.1 

Eq. Class Rep:

7PMM

NDB ID:

 7PMQ

PDB ID:

7PMQ 

Release:

2022-09-14

Title:

DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3

Classification:

RNA BINDING PROTEIN

Authors:

Wurm, J.P.

Citation:

Structure of the DEAD-box helicase DbpA in the closed conformation bound to a 42mer RNA.
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.22Å R work:0.227R free:0.263

Equivalence Class: 

NR_all_30013.1 

Eq. Class Rep:

7PMQ

NDB ID:

 7T1N

PDB ID:

7T1N 

Release:

2022-09-14

Title:

Solution structure of 7SK stem-loop 1 with HEXIM Arginine Rich Motif

Classification:

TRANSCRIPTION

Authors:

Pham, V.V., Gao, M., Meagher, J.L., Smith, J.L., D'Souza, V.M.

Citation:

A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.
Commun Biol 5 pp.819 - 819 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_20257.1 

Eq. Class Rep:

7T1N

NDB ID:

 7T1O

PDB ID:

7T1O 

Release:

2022-09-14

Title:

Solution structure of 7SK stem-loop 1 with HIV-1 Tat Subtype G Arginine Rich Motif

Classification:

TRANSCRIPTION

Authors:

Pham, V.V., Gao, M., Meagher, J.L., Smith, J.L., D'Souza, V.M.

Citation:

A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.
Commun Biol 5 pp.819 - 819 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_44951.1 

Eq. Class Rep:

7T1O

NDB ID:

 7T1P

PDB ID:

7T1P 

Release:

2022-09-14

Title:

Solution structure of 7SK stem-loop 1 with HIV-1 Tat Finland Arginine Rich Motif

Classification:

TRANSCRIPTION

Authors:

Pham, V.V., Gao, M., Meagher, J.L., Smith, J.L., D'Souza, V.M.

Citation:

A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.
Commun Biol 5 pp.819 - 819 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_20257.1 

Eq. Class Rep:

7T1N

NDB ID:

 8AF0

PDB ID:

8AF0 

Release:

2022-09-14

Title:

Crystal structure of human angiogenin and RNA duplex

Classification:

RNA BINDING PROTEIN

Authors:

Sievers, K., Ficner, R.

Citation:

Structure of angiogenin dimer bound to double-stranded RNA.
Acta Crystallogr.,Sect.F 78 pp.330 - 337 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.43Å R work:0.205R free:0.268

Equivalence Class: 

NR_all_82438.1 

Eq. Class Rep:

8AF0

NDB ID:

 7PLI

PDB ID:

7PLI 

Release:

2022-09-07

Title:

DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3

Classification:

RNA BINDING PROTEIN

Authors:

Wurm, J.P.

Citation:

DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.213R free:0.246

Equivalence Class: 

NR_all_17943.1 

Eq. Class Rep:

7PLI

NDB ID:

 7VA3

PDB ID:

7VA3 

Release:

2022-09-07

Title:

PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure

Classification:

HYDROLASE

Authors:

Zhang, J., Zhang, Q., Bartlam, M.

Citation:

PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.8Å R work:0.172R free:0.191

Equivalence Class: 

NR_all_98428.2 

Eq. Class Rep:

6N6I

NDB ID:

 7VA6

PDB ID:

7VA6 

Release:

2022-09-07

Title:

PaOrn Oligoribonuclease D11A mutant with RNA GU complex structure

Classification:

HYDROLASE

Authors:

Zhang, J., Zhang, Q., Bartlam, M.

Citation:

PaOrn Oligoribonuclease D11A mutant with RNA GU complex structure
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.166R free:0.195

Equivalence Class: 

NR_all_78372.5 

Eq. Class Rep:

6X1B

NDB ID:

 7U0Y

PDB ID:

7U0Y 

Release:

2022-08-31

Title:

Crystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6

Classification:

IMMUNE SYSTEM/RNA

Authors:

Rees, H.C., Gogacz, W., Li, N.S., Koirala, D., Piccirilli, J.A.

Citation:

Structural Basis for Fluorescence Activation by Pepper RNA.
Acs Chem.Biol. 17 pp.1866 - 1875 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.66Å R work:0.218R free:0.254

Equivalence Class: 

NR_all_80237.1 

Eq. Class Rep:

7SZU

NDB ID:

 7Z4D

PDB ID:

7Z4D 

Release:

2022-08-31

Title:

Crystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrate

Classification:

HYDROLASE

Authors:

Pacesa, M., Loeff, L., Querques, I., Muckenfuss, L.M., Sawicka, M., Jinek, M.

Citation:

R-loop formation and conformational activation mechanisms of Cas9.
Nature 609 pp.191 - 196 2022

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.246R free:0.275

Equivalence Class: 

NR_all_20965.1 

Eq. Class Rep:

4ZT0

NDB ID:

 7LIU

PDB ID:

7LIU 

Release:

2022-08-24

Title:

DDX3X bound to ATP analog and remodeled RNA:DNA hybrid

Classification:

RNA-BINDING PROTEIN/DNA,RNA

Authors:

Enemark, E.J., Yu, S.

Citation:

DDX3X bound to ATP analog and remodeled RNA:DNA hybrid
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.001Å R work:0.209R free:0.241

Equivalence Class: 

NR_all_36410.1 

Eq. Class Rep:

7LIU

NDB ID:

 7PDV

PDB ID:

7PDV 

Release:

2022-08-24

Title:

Crystal structure of RBM5 RRM1-zinc finger in complex with RNA

Classification:

RNA BINDING PROTEIN

Authors:

Soni, K., Jagtap, P.K.A., Sattler, M.

Citation:

Crystal structure of RBM5 RRM1-zinc finger in complex with RNA
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.49Å R work:0.337R free:0.389

Equivalence Class: 

NR_all_49702.1 

Eq. Class Rep:

7PDV

NDB ID:

 7VTI

PDB ID:

7VTI 

Release:

2022-08-24

Title:

Crystal structure of the Cas13bt3-crRNA binary complex

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Nakagawa, R., Kannan, S., Altae-Tran, H., Takeda, S.N., Tomita, A., Hirano, H., Kusakizako, T., Nishizawa, T., Yamashita, K., Zhang, F., Nishimasu, H., Nureki, O.

Citation:

Structure and engineering of the minimal type VI CRISPR-Cas13bt3.
Mol.Cell 82 pp.3178 - 3192.e5 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.89Å R work:0.195R free:0.242

Equivalence Class: 

NR_all_92884.1 

Eq. Class Rep:

7VTI

NDB ID:

 8DZK

PDB ID:

8DZK 

Release:

2022-08-24

Title:

Dbr1 in complex with 5-mer cleavage product

Classification:

HYDROLASE/RNA

Authors:

Clark, N.E., Taylor, A.B.

Citation:

Dbr1 in complex with 5-mer cleavage product
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.177R free:0.209

Equivalence Class: 

NR_all_04798.1 

Eq. Class Rep:

8DZK

NDB ID:

 7V2Z

PDB ID:

7V2Z 

Release:

2022-08-17

Title:

ZIKV NS3helicase in complex with ssRNA and ATP-Mn2+

Classification:

VIRAL PROTEIN

Authors:

Lin, M.M., Yang, H.T.

Citation:

Structural basis of Zika virus helicase in RNA unwinding and ATP hydrolysis
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.10102Å R work:0.188R free:0.239

Equivalence Class: 

NR_all_77411.1 

Eq. Class Rep:

7V2Z

NDB ID:

 7OOO

PDB ID:

7OOO 

Release:

2022-08-03

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG containing an LNA-Amide-LNA modification

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.57Å R work:0.232R free:0.251

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

 7OOS

PDB ID:

7OOS 

Release:

2022-08-03

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.217R free:0.234

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

 7OZZ

PDB ID:

7OZZ 

Release:

2022-08-03

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG with LNA-amide modification

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.2R free:0.236

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

 7SOP

PDB ID:

7SOP 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAUAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.55Å R work:0.194R free:0.22

Equivalence Class: 

NR_all_62371.1 

Eq. Class Rep:

7SOP

NDB ID:

 7SOQ

PDB ID:

7SOQ 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.15Å R work:0.175R free:0.187

Equivalence Class: 

NR_all_65223.6 

Eq. Class Rep:

6Q1H

NDB ID:

 7SOR

PDB ID:

7SOR 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.35Å R work:0.18R free:0.204

Equivalence Class: 

NR_all_65223.6 

Eq. Class Rep:

6Q1H

NDB ID:

 7SOS

PDB ID:

7SOS 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAA RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.25Å R work:0.174R free:0.194

Equivalence Class: 

NR_all_64918.11 

Eq. Class Rep:

7SOS

NDB ID:

 7SOT

PDB ID:

7SOT 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAAAA oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.52Å R work:0.19R free:0.211

Equivalence Class: 

NR_all_26685.1 

Eq. Class Rep:

7SOT

NDB ID:

 7SOU

PDB ID:

7SOU 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAAAA polynucleotide

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.45Å R work:0.183R free:0.202

Equivalence Class: 

NR_all_77860.1 

Eq. Class Rep:

7SOU

NDB ID:

 7SOV

PDB ID:

7SOV 

Release:

2022-08-03

Title:

LaM domain of human LARP1 in complex with AAAAAAAAAAA RNA polynucleotide

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

Citation:

Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Nucleic Acids Res. pp. - 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.45Å R work:0.183R free:0.223

Equivalence Class: 

NR_all_42542.1 

Eq. Class Rep:

7SOV

NDB ID:

 7QP2

PDB ID:

7QP2 

Release:

2022-07-20

Title:

1-deazaguanosine modified-RNA Sarcin Ricin Loop

Classification:

RNA

Authors:

Bereiter, R., Renard, E., Breuker, K., Kreutz, C., Ennifar, E., Micura, R.

Citation:

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis.
J.Am.Chem.Soc. 144 pp.10344 - 10352 2022

Experiment:

 X-RAY DIFFRACTION Resolution:0.9Å R work:0.115R free:0.137

Equivalence Class: 

NR_all_94729.9 

Eq. Class Rep:

4NLF

NDB ID:

 7R97

PDB ID:

7R97 

Release:

2022-07-20

Title:

Crystal structure of postcleavge complex of Escherichia coli RNase III

Classification:

HYDROLASE/RNA

Authors:

Dharavath, S., Shaw, G.X., Ji, X.

Citation:

Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg 2+ -ion catalysis.
Rna Biol. 19 pp.908 - 915 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.804Å R work:0.171R free:0.202

Equivalence Class: 

NR_all_52425.2 

Eq. Class Rep:

7R97

NDB ID:

 7RWR

PDB ID:

7RWR 

Release:

2022-07-20

Title:

An RNA aptamer that decreases flavin redox potential

Classification:

RNA

Authors:

Samuelian, J.S., Gremminger, T.J., Song, Z., Poudyal, R.R., Li, J., Zhou, Y., Staller, S.A., Carballo, J.A., Roychowdhury-Saha, M., Chen, S.J., Burke, D.H., Heng, X., Baum, D.A.

Citation:

An RNA aptamer that shifts the reduction potential of metabolic cofactors
Nat.Chem.Biol. pp. - 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_89808.1 

Eq. Class Rep:

7RWR

NDB ID:

 7UCR

PDB ID:

7UCR 

Release:

2022-07-20

Title:

Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA

Classification:

RNA

Authors:

Harp, J.M., Lybrand, T.P., Pallan, P.S., Coates, L., Sullivan, B., Egli, M.

Citation:

Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure.
Nucleic Acids Res. 50 pp.7721 - 7738 2022

Experiment:

 NEUTRON DIFFRACTION Resolution:2.25Å R work:0.254R free:0.298

Equivalence Class: 

NR_all_94729.9 

Eq. Class Rep:

4NLF

NDB ID:

 7U2H

PDB ID:

7U2H 

Release:

2022-07-13

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, aminoacylated P-site fMet-NH-tRNAmet, and deacylated E-site tRNAgly at 2.55A resolution

Classification:

RIBOSOME

Authors:

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

Citation:

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.
Nucleic Acids Res. 50 pp.7669 - 7679 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.219R free:0.262

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

 7U2I

PDB ID:

7U2I 

Release:

2022-07-13

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, aminoacylated P-site fMet-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution

Classification:

RIBOSOME

Authors:

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

Citation:

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.
Nucleic Acids Res. 50 pp.7669 - 7679 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.222R free:0.267

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

 7U2J

PDB ID:

7U2J 

Release:

2022-07-13

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, peptidyl P-site fMAC-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution

Classification:

RIBOSOME

Authors:

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

Citation:

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.
Nucleic Acids Res. 50 pp.7669 - 7679 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.213R free:0.256

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

 7F8Z

PDB ID:

7F8Z 

Release:

2022-07-06

Title:

RNA kink-turn motif with 2-aminopurine

Classification:

RNA

Authors:

Kondo, J., Miyauchi, T.

Citation:

RNA kink-turn motif with 2-aminopurine
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.175R free:0.228

Equivalence Class: 

NR_all_88157.3 

Eq. Class Rep:

4CS1

NDB ID:

 7R8J

PDB ID:

7R8J 

Release:

2022-07-06

Title:

Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA in the presence of Mg2+

Classification:

HYDROLASE/DNA

Authors:

Shin, Y., Murakami, K.S.

Citation:

Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA in the presence of Mg2+
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.205R free:0.244

NDB ID:

 7SZU

PDB ID:

7SZU 

Release:

2022-07-06

Title:

Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6

Classification:

IMMUNE SYSTEM/RNA

Authors:

Rees, H.C., Gogacz, W., Li, N.S., Koirala, D., Piccirilli, J.A.

Citation:

Structural Basis for Fluorescence Activation by Pepper RNA.
Acs Chem.Biol. 17 pp.1866 - 1875 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.24Å R work:0.219R free:0.262

Equivalence Class: 

NR_all_80237.1 

Eq. Class Rep:

7SZU

NDB ID:

 7UMC

PDB ID:

7UMC 

Release:

2022-07-06

Title:

DENV1 SLA RNA (DenvSLATL)

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Structure of the dengue virus RNA promoter.
Rna 28 pp.1210 - 1223 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_57150.1 

Eq. Class Rep:

7UMC

NDB ID:

 7UMD

PDB ID:

7UMD 

Release:

2022-07-06

Title:

DENV1 SLA three-way junction RNA (DenvSLAsh)

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Structure of the dengue virus RNA promoter.
Rna 28 pp.1210 - 1223 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_81668.1 

Eq. Class Rep:

7UMD

NDB ID:

 7UME

PDB ID:

7UME 

Release:

2022-07-06

Title:

DENV1 SLA top stemloop RNA (DenvTSL)

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Structure of the dengue virus RNA promoter.
Rna 28 pp.1210 - 1223 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_09835.1 

Eq. Class Rep:

7UME

NDB ID:

 7V06

PDB ID:

7V06 

Release:

2022-06-29

Title:

Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for differential binding of hnRNP Splicing Auxiliary Factors

Classification:

RNA

Authors:

Chiu, L.Y., Emery, A., Jain, N., Sugarman, A., Kendrick, N., Luo, L., Ford, W., Swanstrom, R., Tolbert, B.S.

Citation:

Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors.
J.Mol.Biol. pp.167728 - 167728 2022

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_28070.1 

Eq. Class Rep:

7V06

NDB ID:

 7F3I

PDB ID:

7F3I 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.25Å R work:0.184R free:0.245

Equivalence Class: 

NR_all_19366.1 

Eq. Class Rep:

7F3I

NDB ID:

 7F3J

PDB ID:

7F3J 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.95Å R work:0.187R free:0.228

Equivalence Class: 

NR_all_41208.1 

Eq. Class Rep:

7F3J

NDB ID:

 7F3K

PDB ID:

7F3K 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.76Å R work:0.145R free:0.175

Equivalence Class: 

NR_all_59550.1 

Eq. Class Rep:

7F3K

NDB ID:

 7F3L

PDB ID:

7F3L 

Release:

2022-06-22

Title:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P62

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhang, Y., Huang, Y.

Citation:

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P62
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.88Å R work:0.194R free:0.231

Equivalence Class: 

NR_all_87638.1 

Eq. Class Rep:

5YTV

NDB ID:

 7NRP

PDB ID:

7NRP 

Release:

2022-06-22

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG

Classification:

DNA-RNA HYBRID

Authors:

Baker, Y.R., Thorpe, C., Chen, J., Poller, L.M., Cox, L., Kumar, P., Lim, W.F., Lie, L., McClorey, G., Epple, S., Singleton, D., McDonough, M.A., Hardwick, J.S., Christensen, K.E., Wood, M.J.A., Hall, J.P., El-Sagheer, A.H., Brown, T.

Citation:

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Nat Commun 13 pp.4036 - 4036 2022

Experiment:

 X-RAY DIFFRACTION Resolution:2.67Å R work:0.169R free:0.19

Equivalence Class: 

NR_all_25735.1 

Eq. Class Rep:

1PJG

NDB ID:

 7UQ6

PDB ID:

7UQ6 

Release:

2022-06-15

Title:

tRNA T-box antiterminator fusion, construct #4

Classification:

RNA

Authors:

Grigg, J.C., Price, I.R., Ke, A.

Citation:

tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-box Riboswitch
to be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.951Å R work:0.246R free:0.264

Equivalence Class: 

NR_all_63075.1 

Eq. Class Rep:

7UQ6

NDB ID:

 7VFT

PDB ID:

7VFT 

Release:

2022-06-15

Title:

Crystal structure of rGGGC(CAG)5GUCC oligo

Classification:

RNA

Authors:

An, Y., Chen, Z.S., Chan, H.Y.E., Ngo, J.C.K.

Citation:

Molecular insights into the interaction of CAG trinucleotide RNA repeats with nucleolin and its implication in polyglutamine diseases.
Nucleic Acids Res. 50 pp.7655 - 7668 2022

Experiment:

 X-RAY DIFFRACTION Resolution:1.45Å R work:0.195R free:0.207

Equivalence Class: 

NR_all_41768.1 

Eq. Class Rep:

7VFT

NDB ID:

 7AZS

PDB ID:

7AZS 

Release:

2022-06-08

Title:

70S thermus thermophilus ribosome with bound antibiotic lead SEQ-569

Classification:

RIBOSOME

Authors:

Zhang, J., Lair, C., Roubert, C., Amaning, K., Barrio, M.B., Benedetti, Y., Cui, Z., Li, X., Baurin, N., Bordon-Pallier, F., Cantalloube, C., Sans, S., Blanc, I., Perron, C., Fraisse, L., Rak, A., Jenner, L.B., Yusupova, G., Yusupov, M., Upton, A., Kaneko, T., Yang, T.J., Fotouhi, N., Nuermberger, E., Tyagi, S., Betoudji, F., Sacchettini, J.C., Lagrange, S.

Citation:

Discovery of natural product derived sequanamycins as potent oral anti-tuberculosis agents
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.246R free:0.274

Equivalence Class: 

NR_all_65795.67 

Eq. Class Rep:

4LFB

NDB ID:

 7UZ0

PDB ID:

7UZ0 

Release:

2022-06-08

Title:

AntiT-tRNA flip UCCA

Classification:

RNA

Authors:

Grigg, J.C., Price, I.R., Ke, A.

Citation:

tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-box Riboswitch
To be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.03Å R work:0.246R free:0.276

Equivalence Class: 

NR_all_91710.1 

Eq. Class Rep:

7UZ0

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