[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

TitleConformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity.
Journal, issue, pagesCell, Vol. 175, Issue 7, Page 1856-1871.e21, Year 2018
Publish dateDec 13, 2018
AuthorsStefano Stella / Pablo Mesa / Johannes Thomsen / Bijoya Paul / Pablo Alcón / Simon B Jensen / Bhargav Saligram / Matias E Moses / Nikos S Hatzakis / Guillermo Montoya /
PubMed AbstractCas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures ...Cas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures of intermediates of the cleavage reaction, thus visualizing three protein regions that sense the crRNA-DNA hybrid assembly triggering the catalytic activation of Cas12a. Single-molecule FRET provides the thermodynamics and kinetics of the conformational activation leading to phosphodiester bond hydrolysis. These findings illustrate why Cas12a cuts its target DNA and unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. In addition, we show that other crRNAs are able to displace the R-loop inside the protein after target DNA cleavage, terminating indiscriminate ssDNA degradation. We propose a model whereby the conformational activation of the enzyme results in indiscriminate ssDNA cleavage. The displacement of the R-loop by a new crRNA molecule will reset Cas12a specificity, targeting new DNAs.
External linksCell / PubMed:30503205
MethodsEM (single particle)
Resolution3.27 - 4.24 Å
Structure data

0061

6gtc

EMDB-0061, PDB-6gtc:
Transition state structure of Cpf1(Cas12a) I1 conformation
Method: EM (single particle) / Resolution: 3.91 Å

0062

6gtd

EMDB-0062, PDB-6gtd:
Transient state structure of CRISPR-Cpf1 (Cas12a) I2 conformation
Method: EM (single particle) / Resolution: 4.24 Å

0063

6gte

EMDB-0063, PDB-6gte:
Transient state structure of CRISPR-Cpf1 (Cas12a) I3 conformation
Method: EM (single particle) / Resolution: 4.07 Å

0064

6gtf

EMDB-0064: Transition state I5 crispr-cpf1
PDB-6gtf: Transient state structure of CRISPR-Cpf1 (Cas12a) I5 conformation
Method: EM (single particle) / Resolution: 3.63 Å

0065

6gtg

EMDB-0065, PDB-6gtg:
Transition state structure of Cpf1(Cas12a) I4 conformation
Method: EM (single particle) / Resolution: 3.27 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • francisella tularensis subsp. novicida u112 (bacteria)
  • francisella tularensis subsp. novicida (strain u112) (bacteria)
KeywordsHYDROLASE / genome editing CRISPR ribonucleoprotein complex / CRISPR genome editing ribonucleoprotein complex

+
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