[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 variation of types IV-A1- and IV-A3-mediated CRISPR interference.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 9306, Year 2024
Publish dateOct 29, 2024
AuthorsR Čepaitė / N Klein / A Mikšys / S Camara-Wilpert / V Ragožius / F Benz / A Skorupskaitė / H Becker / G Žvejytė / N Steube / G K A Hochberg / L Randau / R Pinilla-Redondo / L Malinauskaitė / P Pausch /
PubMed AbstractCRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general ...CRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for gene regulation and plasmid competition. To understand how the type IV-A system associated effector complex achieves this interference, we determine cryo-EM structures of two evolutionarily distinct type IV-A complexes (types IV-A1 and IV-A3) bound to cognate DNA-targets in the presence and absence of the type IV-A signature DinG effector helicase. The structures reveal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form an R-loop structure. Additionally, we reveal differences between types IV-A1 and IV-A3 in DNA interactions and structural motifs that allow for in trans recruitment of DinG. Our study provides a detailed view of type IV-A mediated DNA-interference and presents a structural foundation for engineering type IV-A-based genome editing tools.
External linksNat Commun / PubMed:39468082 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 4.8 Å
Structure data

19045

8rc2

EMDB-19045, PDB-8rc2:
DNA bound type IV-A3 CRISPR effector complex from K. pneumoniae
Method: EM (single particle) / Resolution: 3.1 Å

19046

8rc3

EMDB-19046, PDB-8rc3:
DNA bound type IV-A1 CRISPR effector complex from P. oleovorans
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-19120: DNA bound type IV-A1 CRISPR effector complex from P. oleovorans, main body
Method: EM (single particle) / Resolution: 2.96 Å

EMDB-19124: DNA bound type IV-A1 CRISPR effector complex from P. oleovorans Cas6 focused map
Method: EM (single particle) / Resolution: 3.93 Å

19125

8rfj

EMDB-19125, PDB-8rfj:
DNA bound type IV-A1 CRISPR effector complex with the DinG helicase from P. oleovorans
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-19126: Main density of the DNA bound type IV-A1 CRISPR effector complex with the DinG helicase from P. oleovorans
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-19127: DinG focused map of DNA bound type IV-A1 CRISPR effector complex with the DinG helicase from P. oleovorans
Method: EM (single particle) / Resolution: 4.18 Å

19688

8s35

EMDB-19688, PDB-8s35:
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state I)
Method: EM (single particle) / Resolution: 2.9 Å

19689

8s36

EMDB-19689, PDB-8s36:
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state II)
Method: EM (single particle) / Resolution: 2.9 Å

19690

8s37

EMDB-19690, PDB-8s37:
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state III)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-51026: Focused map of Cas6 of the CRISPR type IV-A1 DinG bound complex
Method: EM (single particle) / Resolution: 4.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • klebsiella pneumoniae (bacteria)
  • pseudomonas oleovorans (bacteria)
KeywordsGENE REGULATION / CRISPR / crRNA / DNA binding / type IV CRISPR-Cas / CRISPRi / nuclease deficient / ANTIVIRAL PROTEIN

+
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