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As of 25-May-2022 number of released structures: 12098
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4506  Download results as an excel file       Gallery view

NDB ID:

7S3A

PDB ID:

7S3A 

Release:

2022-05-25

Title:

Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A., Cavendar, C.E., Tebaldi, T., Jenkins, J.L., Mathews, D.H., Halene, S., Kielkopf, C.L.

Citation:

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of Nucleotide variants at the center of the pre-mRNA splice site signal
Nucleic Acids Res. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.48Å R work:0.13R free:0.157

NDB ID:

7S3B

PDB ID:

7S3B 

Release:

2022-05-25

Title:

Crystal structure of intact U2AF65 RRM-region bound to AdML-G5 oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A., Cavendar, C.E., Tebaldi, T., Jenkins, J.L., Mathews, D.H., Halene, S., Kielkopf, C.L.

Citation:

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of Nucleotide variants at the center of the pre-mRNA splice site signal
Nucleic Acids Res. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.89Å R work:0.173R free:0.199

NDB ID:

7S3C

PDB ID:

7S3C 

Release:

2022-05-25

Title:

Crystal structure of intact U2AF65 RRM-region bound to AdML-A5 oligonucleotide

Classification:

RNA BINDING PROTEIN/RNA/DNA

Authors:

Glasser, E., Maji, D., Biancon, G., Puthenpeedikakkal, A., Cavendar, C.E., Tebaldi, T., Jenkins, J.L., Mathews, D.H., Halene, S., Kielkopf, C.L.

Citation:

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of Nucleotide variants at the center of the pre-mRNA splice site signal
Nucleic Acids Res. pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.51Å R work:0.158R free:0.19

NDB ID:

7TZR

PDB ID:

7TZR 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch bound to N-methyl-1-(quinoxalin-6-yl)methanamine (compound 16)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.203R free:0.26

NDB ID:

7TZS

PDB ID:

7TZS 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch in complex with quinoxalin-6-ylmethanamine (compound 17)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.21Å R work:0.204R free:0.244

NDB ID:

7TZT

PDB ID:

7TZT 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.96Å R work:0.243R free:0.256

NDB ID:

7TZU

PDB ID:

7TZU 

Release:

2022-05-25

Title:

Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38)

Classification:

RNA

Authors:

Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aube, J., Weeks, K.M.

Citation:

SHAPE-enabled fragment-based ligand discovery for RNA.
Proc.Natl.Acad.Sci.USA 119 pp.e2122660119 - e2122660119 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.87Å R work:0.229R free:0.269

NDB ID:

7MW8

PDB ID:

7MW8 

Release:

2022-05-18

Title:

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

Classification:

HYDROLASE

Authors:

Fernandez, D., Li, L., Brown, J.A.

Citation:

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.242R free:0.303

Equivalence Class: 

NR_all_81965.1 

Eq. Class Rep:

6N6D

NDB ID:

7Z42

PDB ID:

7Z42 

Release:

2022-05-18

Title:

Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B

Classification:

RNA BINDING PROTEIN

Authors:

Krischuns, T., Isel, C., Drncova, P., Lukarska, M., Pflug, A., Paisant, S., Navratil, V., Cusack, S., Naffakh, N.

Citation:

Type B and Type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.418Å R work:0.223R free:0.256

Equivalence Class: 

NR_all_43130.1 

Eq. Class Rep:

7Z42

NDB ID:

7Z43

PDB ID:

7Z43 

Release:

2022-05-11

Title:

Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B

Classification:

RNA BINDING PROTEIN

Authors:

Krischuns, T., Isel, C., Drncova, P., Lukarska, M., Pflug, A., Paisant, S., Navratil, V., Cusack, S., Naffakh, N.

Citation:

Type B and Type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.123Å R work:0.239R free:0.272

Equivalence Class: 

NR_all_45043.4 

Eq. Class Rep:

4WRT

NDB ID:

7Z4O

PDB ID:

7Z4O 

Release:

2022-05-11

Title:

Influenza A/H7N9 polymerase core dimer with Pol II pSer5 CTD peptide mimic bound in site 2A

Classification:

RNA BINDING PROTEIN

Authors:

Krischuns, T., Isel, C., Drncova, P., Lukarska, M., Pflug, A., Paisant, S., Navratil, V., Cusack, S., Naffakh, N.

Citation:

Type B and Type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.412Å R work:0.22R free:0.272

Equivalence Class: 

NR_all_56731.1 

Eq. Class Rep:

7Z4O

NDB ID:

7Q4L

PDB ID:

7Q4L 

Release:

2022-05-04

Title:

The solution structure of hsDND1 RRM12 bound to CUUAUUUG RNA

Classification:

RNA BINDING PROTEIN

Authors:

Duszczyk, M.M., Wischnewski, H., Kazeeva, T., Arora, R., Loughlin, F.E., von Schroetter, C., Pradere, U., Hall, J., Ciaudo, C., Allain, F.H.-T.

Citation:

The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA regulation
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_08626.1 

Eq. Class Rep:

7Q4L

NDB ID:

7VNV

PDB ID:

7VNV 

Release:

2022-05-04

Title:

Crystal Structure of tRNAVal from Sulfolobus Tokodaii

Classification:

RNA

Authors:

Ohira, T., Minowa, K., Sugiyama, K., Yamashita, S., Sakaguchi, Y., Miyauchi, K., Noguchi, R., Kaneko, A., Orita, I., Fukui, T., Tomita, K., Suzuki, T.

Citation:

Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature 605 pp.372 - 379 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.194R free:0.219

Equivalence Class: 

NR_all_00196.1 

Eq. Class Rep:

7VNV

NDB ID:

7VNW

PDB ID:

7VNW 

Release:

2022-05-04

Title:

Crystal Structure of tRNAVal from Sulfolobus Tokodaii(Dephosphorylated)

Classification:

RNA

Authors:

Ohira, T., Minowa, K., Sugiyama, K., Yamashita, S., Sakaguchi, Y., Miyauchi, K., Noguchi, R., Kaneko, A., Orita, I., Fukui, T., Tomita, K., Suzuki, T.

Citation:

Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature 605 pp.372 - 379 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.61Å R work:0.223R free:0.26

Equivalence Class: 

NR_all_00196.1 

Eq. Class Rep:

7VNV

NDB ID:

7ZEX

PDB ID:

7ZEX 

Release:

2022-05-04

Title:

RNA binding induces an allosteric switch in Cyp33 to repress MLL1 mediated transcription regulation

Classification:

TRANSCRIPTION

Authors:

Blatter, M., Allain, F., Meylan, C.

Citation:

RNA binding induces an allosteric switch in Cyp33 to repress MLL1 mediated transcription regulation
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_13814.1 

Eq. Class Rep:

7ZEX

NDB ID:

7THB

PDB ID:

7THB 

Release:

2022-04-27

Title:

Crystal structure of an RNA-5'/DNA-3' strand exchange junction

Classification:

DNA-RNA HYBRID

Authors:

Cofsky, J.C., Knott, G.J., Gee, C.L., Doudna, J.A.

Citation:

Crystal structure of an RNA/DNA strand exchange junction.
Plos One 17 pp.e0263547 - e0263547 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.64Å R work:0.236R free:0.284

Equivalence Class: 

NR_all_46712.1 

Eq. Class Rep:

7THB

NDB ID:

6YMC

PDB ID:

6YMC 

Release:

2022-04-20

Title:

26-mer stem-loop RNA

Classification:

RNA

Authors:

Niedner, A., Hennig, J., Hofweber, M., Monecke, T., Davydova, E., Gerber, A.P., Anosova, I., Mueller, M., Heym, R., Janowski, R., Paillart, J.-C., Dormann, D., Sattler, M., Niessing, D.

Citation:

Multiple intrinsically disordered RNA-binding motifs cooperate as RNA-folding catalyst and mediate phase transition
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.175R free:0.24

Equivalence Class: 

NR_all_04166.1 

Eq. Class Rep:

6YMC

NDB ID:

7ENI

PDB ID:

7ENI 

Release:

2022-04-20

Title:

Crystal structure of cas and anti-cas protein complex

Classification:

VIRAL PROTEIN/RNA

Authors:

Wang, Y., Li, X.

Citation:

Crystal structure of cas and anti-cas protein complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.632Å R work:0.199R free:0.237

Equivalence Class: 

NR_all_38681.1 

Eq. Class Rep:

7ENI

NDB ID:

7ENR

PDB ID:

7ENR 

Release:

2022-04-20

Title:

Crystal structure of cas and anti-cas protein complex

Classification:

VIRAL PROTEIN/RNA

Authors:

Wang, Y., Li, X.

Citation:

Crystal structure of cas and anti-cas protein complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:4.205Å R work:0.26R free:0.306

Equivalence Class: 

NR_all_28556.1 

Eq. Class Rep:

7ENR

NDB ID:

7N2M

PDB ID:

7N2M 

Release:

2022-04-20

Title:

Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and template/primer having T-C mismatch at the post-insertion site

Classification:

TRANSFERASE/DNA/RNA

Authors:

Baranovskiy, A.G., Babayeva, N.D., Lisova, A.E., Morstadt, L.M., Tahirov, T.H.

Citation:

Structural and functional insight into mismatch extension by human DNA polymerase alpha
Proc.Natl.Acad.Sci.USA pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.194R free:0.228

Equivalence Class: 

NR_all_91665.5 

Eq. Class Rep:

4QCL

NDB ID:

7P0V

PDB ID:

7P0V 

Release:

2022-04-20

Title:

Crystal structure of human SF3A1 ubiquitin-like domain in complex with U1 snRNA stem-loop 4

Classification:

RNA BINDING PROTEIN

Authors:

de Vries, T., Martelly, W., Campagne, S., Sabath, K., Sarnowski, C.P., Wong, J., Leitner, A., Jonas, S., Sharma, S., Allain, F.H.

Citation:

Sequence-specific RNA recognition by an RGG motif connects U1 and U2 snRNP for spliceosome assembly.
Proc.Natl.Acad.Sci.USA 119 pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:1.56Å R work:0.217R free:0.257

Equivalence Class: 

NR_all_12063.1 

Eq. Class Rep:

7P0V

NDB ID:

7EFG

PDB ID:

7EFG 

Release:

2022-04-13

Title:

RNA kink-turn motif

Classification:

RNA

Authors:

Kondo, J., Nagashima, M.

Citation:

RNA kink-turn motif
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.185R free:0.239

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7RZZ

PDB ID:

7RZZ 

Release:

2022-04-13

Title:

Crystal structure of FBF-2 in complex with LST-1 site A peptide and compact FBE RNA

Classification:

RNA BINDING PROTEIN

Authors:

Qiu, C., Wine, R.N., Campbell, Z.T., Hall, T.M.T.

Citation:

Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal.
Nucleic Acids Res. 50 pp.536 - 548 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.39Å R work:0.171R free:0.215

Equivalence Class: 

NR_all_14742.1 

Eq. Class Rep:

7RZZ

NDB ID:

7UGA

PDB ID:

7UGA 

Release:

2022-04-13

Title:

Solution structure of NPSL2

Classification:

RNA

Authors:

Liu, Y., Munsayac, A., Hall, I., Keane, S.C.

Citation:

Solution structure of NPSL2, a regulatory element in the oncomiR-1 RNA
Biorxiv pp. - 2022

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_84981.1 

Eq. Class Rep:

7UGA

NDB ID:

7ZEW

PDB ID:

7ZEW 

Release:

2022-04-13

Title:

RNA binding induces an allosteric switch in Cyp33 to repress MLL1 mediated transcription regulation

Classification:

TRANSCRIPTION

Authors:

Blatter, M., Allain, F.

Citation:

RNA binding induces an allosteric switch in Cyp33 to repress MLL1 mediated transcription regulation
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_13295.1 

Eq. Class Rep:

7ZEW

NDB ID:

7EIU

PDB ID:

7EIU 

Release:

2022-04-06

Title:

Crystal structure of Mei2 RRM3 in complex with 8mer meiRNA

Classification:

RNA BINDING PROTEIN

Authors:

Shen, S., Jian, Y., Cai, Z., Li, F., Lv, M., Liu, Y., Wu, J., Fu, C., Shi, Y.

Citation:

Structural insights reveal the specific recognition of meiRNA by the Mei2 protein.
J Mol Cell Biol pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.349Å R work:0.181R free:0.224

Equivalence Class: 

NR_all_43624.1 

Eq. Class Rep:

7EIU

NDB ID:

7EFI

PDB ID:

7EFI 

Release:

2022-03-30

Title:

RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA

Classification:

DNA-RNA HYBRID

Authors:

Kondo, J., Nagashima, M.

Citation:

RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.192R free:0.233

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7EI5

PDB ID:

7EI5 

Release:

2022-03-30

Title:

GNRA tetraloop receptor motif composed of RNA and DNA

Classification:

DNA-RNA HYBRID

Authors:

Kondo, J., Hayasaka, A.

Citation:

RNA GNRA tetraloop and tetraloop receptor motifs
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.172R free:0.199

NDB ID:

7EI6

PDB ID:

7EI6 

Release:

2022-03-30

Title:

GNRA tetraloop receptor motif composed of RNA and DNA

Classification:

DNA-RNA HYBRID

Authors:

Kondo, J., Hayasaka, A.

Citation:

RNA GNRA tetraloop and tetraloop receptor motifs
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.164R free:0.201

NDB ID:

7EI7

PDB ID:

7EI7 

Release:

2022-03-30

Title:

RNA kink-turn motif with 2-aminopurine

Classification:

RNA

Authors:

Kondo, J., Saisu, S.

Citation:

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

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.245R free:0.304

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7EI8

PDB ID:

7EI8 

Release:

2022-03-30

Title:

RNA kink-turn motif with 2-aminopurine

Classification:

RNA

Authors:

Kondo, J., Saisu, S.

Citation:

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

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.196R free:0.257

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7EI9

PDB ID:

7EI9 

Release:

2022-03-30

Title:

RNA kink-turn motif with pyrrolo cytosine

Classification:

RNA

Authors:

Kondo, J., Miyauchi, T.

Citation:

RNA kink-turn motif with pyrrolo cytosine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.226R free:0.246

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7EIA

PDB ID:

7EIA 

Release:

2022-03-30

Title:

RNA kink-turn motif with pyrrolo cytosine

Classification:

RNA

Authors:

Kondo, J., Miyauchi, T.

Citation:

RNA kink-turn motif with pyrrolo cytosine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.2R free:0.267

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7OUO

PDB ID:

7OUO 

Release:

2022-03-30

Title:

Crystal structure of RNA duplex [UCGUGCGA]2 in complex with Ba2+ cation

Classification:

RNA

Authors:

Ruszkowska, A., Zheng, Y.Y., Mao, S., Ruszkowski, M., Sheng, J.

Citation:

Structural Insights Into the 5'UG/3'GU Wobble Tandem in Complex With Ba 2+ Cation.
Front Mol Biosci 8 pp.762786 - 762786 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.212Å R work:0.233R free:0.285

Equivalence Class: 

NR_all_25020.1 

Eq. Class Rep:

7OUO

NDB ID:

7TQB

PDB ID:

7TQB 

Release:

2022-03-30

Title:

Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid

Classification:

IMMUNE SYSTEM/DNA-RNA HYBRID

Authors:

Bou-Nader, C., Bothra, A., Garboczi, D.N., Leppla, S.H., Zhang, J.

Citation:

Structural basis of R-loop recognition by the S9.6 monoclonal antibody.
Nat Commun 13 pp.1641 - 1641 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.229R free:0.271

Equivalence Class: 

NR_all_45405.1 

Eq. Class Rep:

7TQB

NDB ID:

7V4G

PDB ID:

7V4G 

Release:

2022-03-30

Title:

Crystal structure of human ALKBH5 in complex with m6A-containing ssRNA

Classification:

OXIDOREDUCTASE/RNA

Authors:

Kaur, S., Tam, N.Y., McDonough, M.A., Schofield, C.J., Aik, W.S.

Citation:

Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Nucleic Acids Res. 50 pp.4148 - 4160 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.185R free:0.223

Equivalence Class: 

NR_all_00883.1 

Eq. Class Rep:

7V4G

NDB ID:

7WKV

PDB ID:

7WKV 

Release:

2022-03-30

Title:

Crystal structure of human ALKBH5 in complex with 2-oxoglutarate (2OG) and m6A-containing ssRNA

Classification:

OXIDOREDUCTASE/RNA

Authors:

Kaur, S., Tam, N.Y., McDonough, M.A., Schofield, C.J., Aik, W.S.

Citation:

Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Nucleic Acids Res. 50 pp.4148 - 4160 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.187R free:0.227

Equivalence Class: 

NR_all_00883.1 

Eq. Class Rep:

7V4G

NDB ID:

7WL0

PDB ID:

7WL0 

Release:

2022-03-30

Title:

Crystal structure of human ALKBH5 in complex with N-oxalylglycine (NOG) and m6A-containing ssRNA

Classification:

OXIDOREDUCTASE/RNA

Authors:

Kaur, S., Tam, N.Y., McDonough, M.A., Schofield, C.J., Aik, W.S.

Citation:

Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Nucleic Acids Res. 50 pp.4148 - 4160 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.196R free:0.24

Equivalence Class: 

NR_all_00883.1 

Eq. Class Rep:

7V4G

NDB ID:

7EDT

PDB ID:

7EDT 

Release:

2022-03-23

Title:

RNA duplex containing CC mispairs

Classification:

RNA

Authors:

Kondo, J., Tada, Y.

Citation:

RNA duplex containing CC mispairs
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.2Å R work:0.143R free:0.176

Equivalence Class: 

NR_all_73125.1 

Eq. Class Rep:

7EDT

NDB ID:

7EDU

PDB ID:

7EDU 

Release:

2022-03-23

Title:

RNA duplex containing C-Au-C base pair

Classification:

RNA

Authors:

Kondo, J., Iwase, E.

Citation:

RNA duplex containing C-Au-C base pair
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.176R free:0.229

Equivalence Class: 

NR_all_49464.2 

Eq. Class Rep:

5AY2

NDB ID:

7EEM

PDB ID:

7EEM 

Release:

2022-03-23

Title:

RNA bulged-G motif

Classification:

RNA

Authors:

Kondo, J., Sekiguchi, S.

Citation:

RNA bulged-G motif
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.593Å R work:0.179R free:0.243

Equivalence Class: 

NR_all_94729.8 

Eq. Class Rep:

4NLF

NDB ID:

7EEN

PDB ID:

7EEN 

Release:

2022-03-23

Title:

Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA

Classification:

DNA-RNA HYBRID

Authors:

Kondo, J., Sekiguchi, S.

Citation:

Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.7Å R work:0.188R free:0.237

Equivalence Class: 

NR_all_94729.8 

Eq. Class Rep:

4NLF

NDB ID:

7EEO

PDB ID:

7EEO 

Release:

2022-03-23

Title:

Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA

Classification:

DNA-RNA HYBRID

Authors:

Kondo, J., Sekiguchi, S.

Citation:

Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.701Å R work:0.206R free:0.264

Equivalence Class: 

NR_all_94729.8 

Eq. Class Rep:

4NLF

NDB ID:

7EFH

PDB ID:

7EFH 

Release:

2022-03-23

Title:

RNA kink-turn motif

Classification:

RNA

Authors:

Kondo, J., Nagashima, M.

Citation:

RNA kink-turn motif
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.229R free:0.246

Equivalence Class: 

NR_all_88157.2 

Eq. Class Rep:

4CS1

NDB ID:

7KQM

PDB ID:

7KQM 

Release:

2022-03-23

Title:

Binary complex of TERT (telomerase reverse transcriptase) with RNA/telomeric DNA hybrid

Classification:

TRANSFERASE/RNA/DNA

Authors:

Choi, W.S., Weng, P.J., Yang, W.

Citation:

Flexibility of telomerase in binding the RNA template and DNA telomeric repeat.
Proc.Natl.Acad.Sci.USA 119 pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.73Å R work:0.193R free:0.231

Equivalence Class: 

NR_all_47834.1 

Eq. Class Rep:

7KQM

NDB ID:

7KQN

PDB ID:

7KQN 

Release:

2022-03-23

Title:

Ternary complex of TERT (telomerase reverse transcriptase) with RNA template, DNA primer, an incoming dGTP and a downstream hybrid duplex

Classification:

TRANSFERASE/RNA/DNA

Authors:

Choi, W.S., Weng, P.J., Yang, W.

Citation:

Flexibility of telomerase in binding the RNA template and DNA telomeric repeat.
Proc.Natl.Acad.Sci.USA 119 pp. - 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.02Å R work:0.167R free:0.187

Equivalence Class: 

NR_all_13603.1 

Eq. Class Rep:

7KQN

NDB ID:

7M3V

PDB ID:

7M3V 

Release:

2022-03-23

Title:

RNA bulged-G motif

Classification:

RNA

Authors:

Kondo, J., Sekiguchi, S.

Citation:

RNA bulged-G motif
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.19Å R work:0.177R free:0.213

Equivalence Class: 

NR_all_94729.8 

Eq. Class Rep:

4NLF

NDB ID:

7Q7X

PDB ID:

7Q7X 

Release:

2022-03-23

Title:

Crystal structure of the methyltransferase-ribozyme 1 (with 1-methyl-adenosine)

Classification:

RNA

Authors:

Scheitl, C.P.M., Mieczkowski, M., Schindelin, H., Hobartner, C.

Citation:

Structure and mechanism of the methyltransferase ribozyme MTR1.
Nat.Chem.Biol. 18 pp.547 - 555 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.212R free:0.255

Equivalence Class: 

NR_all_63923.1 

Eq. Class Rep:

7Q80

NDB ID:

7Q7Y

PDB ID:

7Q7Y 

Release:

2022-03-23

Title:

Crystal structure of the methyltransferase-ribozyme 1 (1-benzyl-adenosine derivative)

Classification:

RNA

Authors:

Scheitl, C.P.M., Mieczkowski, M., Schindelin, H., Hobartner, C.

Citation:

Structure and mechanism of the methyltransferase ribozyme MTR1.
Nat.Chem.Biol. 18 pp.547 - 555 2022

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.197R free:0.244

Equivalence Class: 

NR_all_63923.1 

Eq. Class Rep:

7Q80

NDB ID:

7Q7Z

PDB ID:

7Q7Z 

Release:

2022-03-23

Title:

Crystal structure of the methyltransferase-ribozyme 1 (with 1-benzylamine-adenosine)

Classification:

RNA

Authors:

Scheitl, C.P.M., Mieczkowski, M., Schindelin, H., Hobartner, C.

Citation:

Structure and mechanism of the methyltransferase ribozyme MTR1.
Nat.Chem.Biol. 18 pp.547 - 555 2022

Experiment:

X-RAY DIFFRACTION Resolution:3.26Å R work:0.21R free:0.264

Equivalence Class: 

NR_all_47650.1 

Eq. Class Rep:

7Q80