[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleCRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity.
Journal, issue, pagesMol. Cell, Vol. 75, Page 944-956.e6, Year 2019
Publish dateMar 7, 2019 (structure data deposition date)
AuthorsJia, N. / Jones, R. / Yang, G. / Ouerfelli, O. / Patel, D.J.
External linksMol. Cell / PubMed:31326273
MethodsX-ray diffraction
Resolution1.96 - 2.8 Å
Structure data

PDB-6o6s:
Crystal structure of Apo Csm6
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-6o6t:
Crystal structure of Csm6 H132A mutant
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-6o6v:
Crystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6
Method: X-RAY DIFFRACTION / Resolution: 2.35 Å

PDB-6o6x:
Crystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallization
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-6o6y:
Crystal structure of Csm6 in complex with cyclic-tetraadenylates (cA4) by cocrystallization of Csm6 and cA4
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-6o6z:
Crystal structure of Csm6 H381A in complex with cA4 by cocrystallization of cA4 and Csm6
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6o70:
Crystal structure of Csm6 H132A mutant in complex with cA4 by cocrystallization of cA4 and Csm6 H132A mutant
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6o71:
Crystal structure of Csm6 in complex with cdA4 by soaking cdA4 into Csm6
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-6ov0:
Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-ACK:
2',3'- cyclic AMP

ChemComp-LQJ:
3'-O-[(R)-{[(2S,3aS,4S,6S,6aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine

Source
  • thermococcus onnurineus (archaea)
  • thermococcus onnurineus (strain na1) (archaea)
  • synthetic construct (others)
KeywordsIMMUNE SYSTEM / Type III-A CRISPR-Cas system; Csm6 / immune system/rna / Type III-A CRISPR-Cas system; Csm6 in complex with cA4 / immune system-dna complex / immune system-rna complex / Type III-A CRISPR-Cas system; Csm6 W14A-E337A mutant in complex with cA4 / Type III-A CRISPR-Cas system; Csm6 in complex with cA4 by cocrystallization of Csm6 and cA4 / Type III-A CRISPR-Cas system; Csm6 H132A mutant in complex with cA4 / immune system/dna / Type III-A CRISPR-Cas system; Csm6 in complex with cdA4

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more