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As of 1-Dec-2021 number of released structures: 11785
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4380  Download results as an excel file       Gallery view

NDB ID:

7FHI

PDB ID:

7FHI 

Release:

2021-12-01

Title:

Interaction between a fluoroquinolone derivative and RNAs with a single bulge

Classification:

RNA

Authors:

Nagano, K., Kamimura, T., Kawai, G.

Citation:

Interaction between a fluoroquinolone derivative and RNAs with a single bulge.
J.Biochem. pp. - 2021

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_55691.1 

Eq. Class Rep:

7FHI

NDB ID:

7FJ0

PDB ID:

7FJ0 

Release:

2021-12-01

Title:

Interaction between a fluoroquinolone derivative and RNAs with a single bulge

Classification:

RNA

Authors:

Nagano, K., Kamimura, T., Kawai, G.

Citation:

Interaction between a fluoroquinolone derivative and RNAs with a single bulge.
J.Biochem. pp. - 2021

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_89167.1 

Eq. Class Rep:

7FJ0

NDB ID:

6WW6

PDB ID:

6WW6 

Release:

2021-11-24

Title:

Crystal structure of EutV bound to RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Ataide, S.F., Walshe, J.L.

Citation:

One by one: Structural characterisation of an RNA bound anti-terminator protein reveals a successive binding mode
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.8Å R work:0.233R free:0.241

Equivalence Class: 

NR_all_24584.1 

Eq. Class Rep:

6WW6

NDB ID:

7EOG

PDB ID:

7EOG 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC, iridium hexammine soak

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.192R free:0.218

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOH

PDB ID:

7EOH 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.637Å R work:0.197R free:0.232

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOI

PDB ID:

7EOI 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC, manganese soak

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.92Å R work:0.215R free:0.243

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOJ

PDB ID:

7EOJ 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC, cesium soak

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.77Å R work:0.207R free:0.215

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOK

PDB ID:

7EOK 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC485

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.201R free:0.241

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOL

PDB ID:

7EOL 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC497

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.309Å R work:0.218R free:0.267

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOM

PDB ID:

7EOM 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC508

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.703Å R work:0.22R free:0.265

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EON

PDB ID:

7EON 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC514

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.211R free:0.261

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOO

PDB ID:

7EOO 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC525

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.23Å R work:0.227R free:0.254

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

7EOP

PDB ID:

7EOP 

Release:

2021-11-24

Title:

Crystal structure of the Pepper aptamer in complex with HBC620

Classification:

RNA

Authors:

Huang, K., Chen, X., Li, C., Song, Q., Li, H., Zhu, L., Yang, Y., Ren, A.

Citation:

Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol. pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.189R free:0.211

Equivalence Class: 

NR_all_54098.1 

Eq. Class Rep:

7EOG

NDB ID:

6WXQ

PDB ID:

6WXQ 

Release:

2021-11-17

Title:

Crystal structure of CRISPR-associated transcription factor Csa3 complexed with cA4

Classification:

TRANSCRIPTION

Authors:

Xia, P., Dutta, A., Parashar, V.

Citation:

Crystal structure of CRISPR-associated transcription factor-ligand complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.05Å R work:0.159R free:0.205

Equivalence Class: 

NR_all_64918.10 

Eq. Class Rep:

6SCE

NDB ID:

7E9E

PDB ID:

7E9E 

Release:

2021-11-17

Title:

Crystal structure of a class I PreQ1 riboswitch aptamer (ab13-14) complexed with a cognate ligand-derived photoaffinity probe

Classification:

RNA

Authors:

Balaratnam, S., Rhodes, C., Bume, D.D., Connelly, C., Lai, C.C., Kelley, J.A., Yazdani, K., Homan, P.J., Incarnato, D., Numata, T., Schneekloth Jr., J.S.

Citation:

A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites.
Nat Commun 12 pp.5856 - 5856 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.57Å R work:0.19R free:0.208

Equivalence Class: 

NR_all_80276.3 

Eq. Class Rep:

6E1S

NDB ID:

7E9I

PDB ID:

7E9I 

Release:

2021-11-17

Title:

Crystal structure of a class I PreQ1 riboswitch aptamer (wild-type) complexed with a cognate ligand-derived photoaffinity probe

Classification:

RNA

Authors:

Balaratnam, S., Rhodes, C., Bume, D.D., Connelly, C., Lai, C.C., Kelley, J.A., Yazdani, K., Homan, P.J., Incarnato, D., Numata, T., Schneekloth Jr., J.S.

Citation:

A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites.
Nat Commun 12 pp.5856 - 5856 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.193R free:0.234

Equivalence Class: 

NR_all_80276.3 

Eq. Class Rep:

6E1S

NDB ID:

7DLZ

PDB ID:

7DLZ 

Release:

2021-10-27

Title:

Crystal Structure of Methyltransferase Ribozyme

Classification:

TRANSFERASE/RNA

Authors:

Jiang, H.Y., Gao, Y.Q., Zhang, L., Chen, D.R., Gan, J.H., Murchie, A.I.H.

Citation:

The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences
Nat Catal 4 pp.872 - 881 2021

Experiment:

X-RAY DIFFRACTION Resolution:3.002Å R work:0.212R free:0.266

Equivalence Class: 

NR_all_56532.1 

Eq. Class Rep:

7DLZ

NDB ID:

7DWH

PDB ID:

7DWH 

Release:

2021-10-27

Title:

Complex structure of SAM-dependent methyltransferase ribozyme

Classification:

TRANSFERASE/RNA

Authors:

Jiang, H.Y., Gao, Y.Q., Zhang, L., Chen, D.R., Gan, J.H., Murchie, A.I.H.

Citation:

The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences
Nat Catal 4 pp.872 - 881 2021

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.208R free:0.258

Equivalence Class: 

NR_all_56532.1 

Eq. Class Rep:

7DLZ

NDB ID:

7OFW

PDB ID:

7OFW 

Release:

2021-10-27

Title:

Nontypeable Haemophillus influenzae SapA in complex with heme

Classification:

PEPTIDE BINDING PROTEIN

Authors:

Lukacik, P., Owen, C.D., Harris, G., Bolla, J.R., Picaud, S., Alibay, I., Nettleship, J.E., Bird, L.E., Owens, R.J., Biggin, P.C., Filippakopoulos, P., Robinson, C.V., Walsh, M.A.

Citation:

The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif.
Plos One 16 pp.e0256070 - e0256070 2021

Experiment:

X-RAY DIFFRACTION Resolution:3.15Å R work:0.242R free:0.281

Equivalence Class: 

NR_all_36586.1 

Eq. Class Rep:

7OFW

NDB ID:

7OFZ

PDB ID:

7OFZ 

Release:

2021-10-27

Title:

Nontypeable Haemophillus influenzae SapA in complex with double stranded RNA

Classification:

PEPTIDE BINDING PROTEIN

Authors:

Lukacik, P., Owen, C.D., Harris, G., Bolla, J.R., Picaud, S., Alibay, I., Nettleship, J.E., Bird, L.E., Owens, R.J., Biggin, P.C., Filippakopoulos, P., Robinson, C.V., Walsh, M.A.

Citation:

The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif.
Plos One 16 pp.e0256070 - e0256070 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.62Å R work:0.216R free:0.263

Equivalence Class: 

NR_all_42626.1 

Eq. Class Rep:

7OFZ

NDB ID:

7OG0

PDB ID:

7OG0 

Release:

2021-10-27

Title:

Nontypeable Haemophillus influenzae SapA in open and closed conformations, in complex with double stranded RNA

Classification:

PEPTIDE BINDING PROTEIN

Authors:

Lukacik, P., Owen, C.D., Harris, G., Bolla, J.R., Picaud, S., Alibay, I., Nettleship, J.E., Bird, L.E., Owens, R.J., Biggin, P.C., Filippakopoulos, P., Robinson, C.V., Walsh, M.A.

Citation:

The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif.
Plos One 16 pp.e0256070 - e0256070 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.61Å R work:0.196R free:0.248

Equivalence Class: 

NR_all_91810.1 

Eq. Class Rep:

7OG0

NDB ID:

7OZQ

PDB ID:

7OZQ 

Release:

2021-10-27

Title:

Crystal structure of archaeal L7Ae bound to eukaryotic kink-loop

Classification:

RIBOSOMAL PROTEIN

Authors:

Hofler, S., Lukat, P., Blankenfeldt, W., Carlomagno, T.

Citation:

Eukaryotic Box C/D methylation machinery has two non-symmetric protein assembly sites.
Sci Rep 11 pp.17561 - 17561 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.91Å R work:0.172R free:0.218

Equivalence Class: 

NR_all_45428.1 

Eq. Class Rep:

7OZQ

NDB ID:

7RQ8

PDB ID:

7RQ8 

Release:

2021-10-13

Title:

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.50A resolution

Classification:

RIBOSOME/RNA

Authors:

Mitcheltree, M.J., Pisipati, A., Syroegin, E.A., Silvestre, K.J., Klepacki, D., Mason, J.D., Terwilliger, D.W., Testolin, G., Pote, A.R., Wu, K.J.Y., Ladley, R.P., Chatman, K., Mankin, A.S., Polikanov, Y.S., Myers, A.G.

Citation:

A synthetic antibiotic scaffold effective against multidrug-resistant bacterial pathogens
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.224R free:0.268

Equivalence Class: 

NR_all_65795.61 

Eq. Class Rep:

4LFB

NDB ID:

7RQ9

PDB ID:

7RQ9 

Release:

2021-10-13

Title:

Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.60A resolution

Classification:

Ribosome/RNA

Authors:

Mitcheltree, M.J., Pisipati, A., Syroegin, E.A., Silvestre, K.J., Klepacki, D., Mason, J.D., Terwilliger, D.W., Testolin, G., Pote, A.R., Wu, K.J.Y., Ladley, R.P., Chatman, K., Mankin, A.S., Polikanov, Y.S., Myers, A.G.

Citation:

A synthetic antibiotic scaffold effective against multidrug-resistant bacterial pathogens
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.24R free:0.297

Equivalence Class: 

NR_all_65795.61 

Eq. Class Rep:

4LFB

NDB ID:

7A18

PDB ID:

7A18 

Release:

2021-10-06

Title:

50S Deinococcus radiodurans ribosome bounded with mycinamicin IV

Classification:

ANTIBIOTIC

Authors:

Breiner, E., Eyal, Z., Matzov, D., Halfon, Y., Cimicata, G., Rozenberg, H., Zimmerman, E., Bashan, A., Yonath, A.

Citation:

50S Deinococcus radiodurans ribosome bounded with mycinamicin IV
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.283R free:0.318

Equivalence Class: 

NR_all_17405.9 

Eq. Class Rep:

7A0S

NDB ID:

7KI3

PDB ID:

7KI3 

Release:

2021-10-06

Title:

Human Argonaute2:miR-122 bound to the HCV genotype 1a site-1 RNA

Classification:

HYDROLASE/RNA

Authors:

Gebert, L.F.R., Law, M., MacRae, I.J.

Citation:

A structured RNA motif locks Argonaute2:miR-122 onto the 5' end of the HCV genome
Nat Commun pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.232R free:0.275

Equivalence Class: 

NR_all_23918.1 

Eq. Class Rep:

7KI3

NDB ID:

7K4L

PDB ID:

7K4L 

Release:

2021-09-29

Title:

Dengue 5'UTR SLA

Classification:

RNA

Authors:

Sun, Y.T., Varani, G.

Citation:

Solution NMR Structure of Denv1 5'UTR SLA region
To Be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_26568.1 

Eq. Class Rep:

7K4L

NDB ID:

7MJV

PDB ID:

7MJV 

Release:

2021-09-15

Title:

MiaB in the complex with s-adenosylmethionine and RNA

Classification:

TRANSFERASE/RNA

Authors:

Esakova, O.A., Grove, T.L., Yennawar, N.H., Arcinas, A.J., Wang, B., Krebs, C., Almo, S.C., Booker, S.J.

Citation:

Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.
Nature 597 pp.566 - 570 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.24Å R work:0.243R free:0.272

Equivalence Class: 

NR_all_67601.1 

Eq. Class Rep:

7MJV

NDB ID:

7MJW

PDB ID:

7MJW 

Release:

2021-09-15

Title:

Methylated MiaB in the complex with 5'-deoxyadenosine, methionine and RNA

Classification:

TRANSFERASE/RNA

Authors:

Esakova, O.A., Grove, T.L., Yennawar, N.H., Arcinas, A.J., Wang, B., Krebs, C., Almo, S.C., Booker, S.J.

Citation:

Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.
Nature 597 pp.566 - 570 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.4Å R work:0.149R free:0.173

Equivalence Class: 

NR_all_31728.1 

Eq. Class Rep:

7MJW

NDB ID:

7MJX

PDB ID:

7MJX 

Release:

2021-09-15

Title:

MiaB in the complex with 5'-deoxyadenosine, methionine and RNA

Classification:

TRANSFERASE/RNA

Authors:

Esakova, O.A., Grove, T.L., Yennawar, N.H., Arcinas, A.J., Wang, B., Krebs, C., Almo, S.C., Booker, S.J.

Citation:

Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.
Nature 597 pp.566 - 570 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.148R free:0.17

Equivalence Class: 

NR_all_31728.1 

Eq. Class Rep:

7MJW

NDB ID:

7MJY

PDB ID:

7MJY 

Release:

2021-09-15

Title:

MiaB in the complex with s-adenosyl-L-homocysteine and RNA

Classification:

TRANSFERASE/RNA

Authors:

Esakova, O.A., Grove, T.L., Yennawar, N.H., Arcinas, A.J., Wang, B., Krebs, C., Almo, S.C., Booker, S.J.

Citation:

Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.
Nature 597 pp.566 - 570 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.86Å R work:0.174R free:0.208

Equivalence Class: 

NR_all_65501.1 

Eq. Class Rep:

7MJY

NDB ID:

7MPL

PDB ID:

7MPL 

Release:

2021-09-15

Title:

Bartonella henselae NrnC bound to pGG

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Lormand, J.D., Kim, S.K., Walters-Marrah, G.A., Brownfield, B.A., Fromme, J.C., Winkler, W.C., Goodson, J.R., Lee, V.T., Sondermann, H.

Citation:

Structural characterization of NrnC identifies unifying features of dinucleotidases.
Elife 10 pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.15R free:0.171

Equivalence Class: 

NR_all_98428.1 

Eq. Class Rep:

6N6I

NDB ID:

7MPM

PDB ID:

7MPM 

Release:

2021-09-15

Title:

Bartonella henselae NrnC bound to pAA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Lormand, J.D., Kim, S.K., Walters-Marrah, G.A., Brownfield, B.A., Fromme, J.C., Winkler, W.C., Goodson, J.R., Lee, V.T., Sondermann, H.

Citation:

Structural characterization of NrnC identifies unifying features of dinucleotidases.
Elife 10 pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.145R free:0.179

Equivalence Class: 

NR_all_53003.1 

Eq. Class Rep:

6N6C

NDB ID:

7MPN

PDB ID:

7MPN 

Release:

2021-09-15

Title:

Bartonella henselae NrnC bound to pGC

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Lormand, J.D., Kim, S.K., Walters-Marrah, G.A., Brownfield, B.A., Fromme, J.C., Winkler, W.C., Goodson, J.R., Lee, V.T., Sondermann, H.

Citation:

Structural characterization of NrnC identifies unifying features of dinucleotidases.
Elife 10 pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.94Å R work:0.194R free:0.224

Equivalence Class: 

NR_all_65789.1 

Eq. Class Rep:

6N6F

NDB ID:

7MPQ

PDB ID:

7MPQ 

Release:

2021-09-15

Title:

Bartonella henselae NrnC cleaving pGG in the presence of Mn2+

Classification:

RNA BINDING PROTEIN

Authors:

Lormand, J.D., Kim, S.K., Walters-Marrah, G.A., Brownfield, B.A., Fromme, J.C., Winkler, W.C., Goodson, J.R., Lee, V.T., Sondermann, H.

Citation:

Structural characterization of NrnC identifies unifying features of dinucleotidases.
Elife 10 pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.35Å R work:0.161R free:0.206

Equivalence Class: 

NR_all_98428.1 

Eq. Class Rep:

6N6I

NDB ID:

7MPU

PDB ID:

7MPU 

Release:

2021-09-15

Title:

Brucella melitensis NrnC bound to pGG

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Lormand, J.D., Kim, S.K., Walters-Marrah, G.A., Brownfield, B.A., Fromme, J.C., Winkler, W.C., Goodson, J.R., Lee, V.T., Sondermann, H.

Citation:

Structural characterization of NrnC identifies unifying features of dinucleotidases.
Elife 10 pp. - 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.72Å R work:0.155R free:0.183

Equivalence Class: 

NR_all_98428.1 

Eq. Class Rep:

6N6I

NDB ID:

7OX7

PDB ID:

7OX7 

Release:

2021-09-15

Title:

Target-bound SpCas9 complex with TRAC chimeric RNA-DNA guide

Classification:

HYDROLASE

Authors:

Donohoue, P.D., Pacesa, M., Lau, E., Vidal, B., Irby, M.J., Nyer, D.B., Rotstein, T., Banh, L., Toh, M.S., Gibson, J., Kohrs, B., Baek, K., Owen, A.L.G., Slorach, E.M., van Overbeek, M., Fuller, C.K., May, A.P., Jinek, M., Cameron, P.

Citation:

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell 81 pp.3637 - 3649.e5 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.209R free:0.229

NDB ID:

7OX8

PDB ID:

7OX8 

Release:

2021-09-15

Title:

Target-bound SpCas9 complex with TRAC full RNA guide

Classification:

HYDROLASE

Authors:

Donohoue, P.D., Pacesa, M., Lau, E., Vidal, B., Irby, M.J., Nyer, D.B., Rotstein, T., Banh, L., Toh, M.S., Gibson, J., Kohrs, B., Baek, K., Owen, A.L.G., Slorach, E.M., van Overbeek, M., Fuller, C.K., May, A.P., Jinek, M., Cameron, P.

Citation:

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell 81 pp.3637 - 3649.e5 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.209R free:0.247

Equivalence Class: 

NR_all_09588.1 

Eq. Class Rep:

7OX8

NDB ID:

7OX9

PDB ID:

7OX9 

Release:

2021-09-15

Title:

Target-bound SpCas9 complex with AAVS1 all-RNA guide

Classification:

HYDROLASE

Authors:

Donohoue, P.D., Pacesa, M., Lau, E., Vidal, B., Irby, M.J., Nyer, D.B., Rotstein, T., Banh, L., Toh, M.S., Gibson, J., Kohrs, B., Baek, K., Owen, A.L.G., Slorach, E.M., van Overbeek, M., Fuller, C.K., May, A.P., Jinek, M., Cameron, P.

Citation:

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell 81 pp.3637 - 3649.e5 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.194R free:0.232

Equivalence Class: 

NR_all_92730.1 

Eq. Class Rep:

7OX9

NDB ID:

7OXA

PDB ID:

7OXA 

Release:

2021-09-15

Title:

Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide

Classification:

HYDROLASE

Authors:

Donohoue, P.D., Pacesa, M., Lau, E., Vidal, B., Irby, M.J., Nyer, D.B., Rotstein, T., Banh, L., Toh, M.S., Gibson, J., Kohrs, B., Baek, K., Owen, A.L.G., Slorach, E.M., van Overbeek, M., Fuller, C.K., May, A.P., Jinek, M., Cameron, P.

Citation:

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell 81 pp.3637 - 3649.e5 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.15Å R work:0.197R free:0.225

NDB ID:

7JRR

PDB ID:

7JRR 

Release:

2021-09-08

Title:

Crystal structures of artificially designed homomeric RNA nanoarchitectures

Classification:

RNA

Authors:

Liu, D., Shao, Y., Piccirilli, J.A., Weizmann, Y.

Citation:

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.
Sci Adv 7 pp.eabf4459 - eabf4459 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.16Å R work:0.226R free:0.259

Equivalence Class: 

NR_all_18633.1 

Eq. Class Rep:

7JRR

NDB ID:

7JRS

PDB ID:

7JRS 

Release:

2021-09-08

Title:

Crystal structures of artificially designed homomeric RNA nanoarchitectures

Classification:

RNA

Authors:

Liu, D., Shao, Y., Piccirilli, J.A., Weizmann, Y.

Citation:

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.
Sci Adv 7 pp.eabf4459 - eabf4459 2021

Experiment:

X-RAY DIFFRACTION Resolution:3.21Å R work:0.274R free:0.296

Equivalence Class: 

NR_all_45061.1 

Eq. Class Rep:

7JRS

NDB ID:

7JRT

PDB ID:

7JRT 

Release:

2021-09-08

Title:

Crystal structures of artificially designed homomeric RNA nanoarchitectures

Classification:

RNA

Authors:

Liu, D., Shao, Y., Piccirilli, J.A., Weizmann, Y.

Citation:

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.
Sci Adv 7 pp.eabf4459 - eabf4459 2021

Experiment:

X-RAY DIFFRACTION Resolution:3.07Å R work:0.188R free:0.226

Equivalence Class: 

NR_all_51052.1 

Eq. Class Rep:

7JRT

NDB ID:

7KUK

PDB ID:

7KUK 

Release:

2021-09-08

Title:

High resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.67Å R work:0.201R free:0.22

Equivalence Class: 

NR_all_01949.4 

Eq. Class Rep:

5UED

NDB ID:

7KUL

PDB ID:

7KUL 

Release:

2021-09-08

Title:

DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.64Å R work:0.207R free:0.246

Equivalence Class: 

NR_all_01949.4 

Eq. Class Rep:

5UED

NDB ID:

7KUM

PDB ID:

7KUM 

Release:

2021-09-08

Title:

LNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.714Å R work:0.205R free:0.22

Equivalence Class: 

NR_all_01949.4 

Eq. Class Rep:

5UED

NDB ID:

7KUN

PDB ID:

7KUN 

Release:

2021-09-08

Title:

2'-F modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.58Å R work:0.193R free:0.23

Equivalence Class: 

NR_all_69465.1 

Eq. Class Rep:

7KUN

NDB ID:

7KUO

PDB ID:

7KUO 

Release:

2021-09-08

Title:

FANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:2.281Å R work:0.203R free:0.263

Equivalence Class: 

NR_all_01949.4 

Eq. Class Rep:

5UED

NDB ID:

7KUP

PDB ID:

7KUP 

Release:

2021-09-08

Title:

2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.44Å R work:0.198R free:0.218

Equivalence Class: 

NR_all_01949.4 

Eq. Class Rep:

5UED

NDB ID:

7LNE

PDB ID:

7LNE 

Release:

2021-09-08

Title:

ANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Classification:

RNA

Authors:

Giurgiu, C., Fang, Z., Aitken, H.R.M., Kim, S.C., Pazienza, L., Mittal, S., Szostak, J.W.

Citation:

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl. 60 pp.22925 - 22932 2021

Experiment:

X-RAY DIFFRACTION Resolution:1.53Å R work:0.191R free:0.225

Equivalence Class: 

NR_all_07962.1 

Eq. Class Rep:

7LNE