[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

TitleSecond Messenger cA Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.
Journal, issue, pagesMol Cell, Vol. 75, Issue 5, Page 933-943.e6, Year 2019
Publish dateSep 5, 2019
AuthorsNing Jia / Roger Jones / George Sukenick / Dinshaw J Patel /
PubMed AbstractTarget RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA) formation from ATP subunits positioned within the composite pair ...Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit. The generated cA second messenger in turn targets the CARF domain of trans-acting RNase Csm6, triggering its HEPN domain-based RNase activity. We have undertaken cryo-EM studies on multi-subunit Thermococcus onnurineus Csm effector ternary complexes, as well as X-ray studies on Csm1-Csm4 cassette, both bound to substrate (AMPPNP), intermediates (pppA), and products (cA), to decipher mechanistic aspects of cA formation and release. A network of intermolecular hydrogen bond alignments accounts for the observed adenosine specificity, with ligand positioning dictating formation of linear pppA intermediates and subsequent cA formation by cyclization. We combine our structural results with published functional studies to highlight mechanistic insights into the role of the Csm effector complex in mediating the cA signaling pathway.
External linksMol Cell / PubMed:31326272 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.4 - 3.2 Å
Structure data

0640

6o7e

EMDB-0640, PDB-6o7e:
Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type III-A CRISPR-Cas system
Method: EM (single particle) / Resolution: 3.2 Å

0641

6o7h

EMDB-0641, PDB-6o7h:
Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system
Method: EM (single particle) / Resolution: 2.9 Å

0642

6o7i

EMDB-0642, PDB-6o7i:
Cryo-EM structure of Csm-crRNA-target RNA ternary bigger complex in complex with cA4 in type III-A CRISPR-Cas system
Method: EM (single particle) / Resolution: 3.2 Å

PDB-6o73:
Crystal structure of apo Csm1-Csm4 cassette
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-6o74:
Crystal structure of Csm1-Csm4 cassette in complex with AMPPNP
Method: X-RAY DIFFRACTION / Resolution: 2.71 Å

PDB-6o75:
Crystal structure of Csm1-Csm4 cassette in complex with pppApA
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6o78:
Crystal structure of Csm1-Csm4 cassette in complex with pppApApA
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6o79:
Crystal structure of Csm1-Csm4 cassette in complex with cA3
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-6o7b:
Crystal structure of Csm1-Csm4 cassette in complex with cA4
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-6o7d:
Crystal structure of Csm1-Csm4 cassette in complex with one ATP
Method: X-RAY DIFFRACTION / Resolution: 2.81 Å

Chemicals

ChemComp-NI:
NICKEL (II) ION

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ZN:
Unknown entry

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

Source
  • thermococcus onnurineus (archaea)
  • thermococcus onnurineus (strain na1) (archaea)
  • thermococcus onnurineus na1 (archaea)
  • synthetic construct (others)
KeywordsIMMUNE SYSTEM / Type III-A CRISPR-Cas system / apo Csm1-Csm4 cassette / aCsm1-Csm4 cassette in complex with AMPPNP / immune system/rna / Csm1-Csm4 cassette in complex with pppApA / immune system-dna complex / immune system-rna complex / Csm1-Csm4 cassette in complex with pppApApA / immune sytem/rna / Csm1-Csm4 cassette in complex with cA3 / immune sytem-rna complex / Csm1-Csm4 cassette in complex with cA4 / Csm1-Csm4 cassette in complex with one ATP / cryo-EM structure / Csm-crRNA-target RNA ternary complex in complex with AMPPNP / Type III CRISPR-Cas systerm / immune system/rna/dna / Csm-crRNA-target RNA ternary complex in complex with CA4 / immune system-rna-dna complex / Csm-crRNA-target RNA ternary bigger complex in complex with CA4

+
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