[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

TitleStructural snapshots of R-loop formation by a type I-C CRISPR Cascade.
Journal, issue, pagesMol Cell, Vol. 83, Issue 5, Page 746-758.e5, Year 2023
Publish dateMar 2, 2023
AuthorsRoisin E O'Brien / Jack P K Bravo / Delisa Ramos / Grace N Hibshman / Jacquelyn T Wright / David W Taylor /
PubMed AbstractType I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various ...Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the "belly" subunits, securing the NTS in place. This "molecular seatbelt" mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity.
External linksMol Cell / PubMed:36805026 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.1 Å
Structure data

27393

8dej

EMDB-27393, PDB-8dej:
D. vulgaris type I-C Cascade bound to dsDNA target
Method: EM (single particle) / Resolution: 2.86 Å

27402

8dex

EMDB-27402, PDB-8dex:
type I-C Cascade
Method: EM (single particle) / Resolution: 2.7 Å

27403

8dfa

EMDB-27403, PDB-8dfa:
type I-C Cascade bound to ssDNA target
Method: EM (single particle) / Resolution: 2.8 Å

27409

8dfo

EMDB-27409, PDB-8dfo:
type I-C Cascade bound to AcrIC4
Method: EM (single particle) / Resolution: 3.1 Å

27412

8dfs

EMDB-27412, PDB-8dfs:
type I-C Cascade bound to AcrIF2
Method: EM (single particle) / Resolution: 3.0 Å

Source
  • desulfovibrio vulgaris (bacteria)
  • synthetic construct (others)
  • desulfovibrio vulgaris str. hildenborough (bacteria)
  • pseudomonas aeruginosa phage dms3mvir (virus)
  • casadabanvirus d3112
KeywordsDNA BINDING PROTEIN/DNA/RNA / type I-C Cascade / dsDNA bound / CRISPR / Cascade / type I-C / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex / ssDNA target / anti-CRISPR / AcrIC4 / IF2

+
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