[English] 日本語
Yorodumi
- PDB-7t3k: Cryo-EM structure of Csy-AcrIF24 dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t3k
TitleCryo-EM structure of Csy-AcrIF24 dimer
Components
  • (CRISPR type I-F/YPEST-associated protein ...) x 2
  • (CRISPR-associated ...) x 2
  • AcrIF24
  • RNA (61-MER)
KeywordsHYDROLASE/RNA / Csy / Cascade / CRISPR / anti-CRISPR / AcrIF24 / HYDROLASE-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR type I-F/YPEST-associated protein Csy3 / CRISPR type I-F/YPEST-associated protein Csy2 / CRISPR-associated protein Csy1 / CRISPR-associated endonuclease Cas6/Csy4
Similarity search - Component
Biological speciesPseudomonas (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMukherjee, I.A. / Chang, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138675 United States
CitationJournal: Nat Chem Biol / Year: 2022
Title: Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor.
Authors: Indranil Arun Mukherjee / Clinton Gabel / Nicholas Noinaj / Joseph Bondy-Denomy / Leifu Chang /
Abstract: Anti-CRISPR (Acr) proteins are encoded by phages to inactivate CRISPR-Cas systems of bacteria and archaea and are used to enhance the CRISPR toolbox for genome editing. Here we report the structure ...Anti-CRISPR (Acr) proteins are encoded by phages to inactivate CRISPR-Cas systems of bacteria and archaea and are used to enhance the CRISPR toolbox for genome editing. Here we report the structure and mechanism of AcrIF24, an Acr protein that inhibits the type I-F CRISPR-Cas system from Pseudomonas aeruginosa. AcrIF24 is a homodimer that associates with two copies of the surveillance complex (Csy) and prevents the hybridization between CRISPR RNA and target DNA. Furthermore, AcrIF24 functions as an anti-CRISPR-associated (Aca) protein to repress the transcription of the acrIF23-acrIF24 operon. Alone or in complex with Csy, AcrIF24 is capable of binding to the acrIF23-acrIF24 promoter DNA with nanomolar affinity. The structure of a Csy-AcrIF24-promoter DNA complex at 2.7 Å reveals the mechanism for transcriptional suppression. Our results reveal that AcrIF24 functions as an Acr-Aca fusion protein, and they extend understanding of the diverse mechanisms used by Acr proteins.
History
DepositionDec 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 7, 2022Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated protein Csy1
B: CRISPR type I-F/YPEST-associated protein Csy2
C: CRISPR-associated endonuclease Cas6/Csy4
D: CRISPR type I-F/YPEST-associated protein Csy3
E: CRISPR type I-F/YPEST-associated protein Csy3
F: CRISPR type I-F/YPEST-associated protein Csy3
G: CRISPR type I-F/YPEST-associated protein Csy3
H: CRISPR type I-F/YPEST-associated protein Csy3
I: CRISPR type I-F/YPEST-associated protein Csy3
J: AcrIF24
K: AcrIF24
M: RNA (61-MER)
a: CRISPR-associated protein Csy1
b: CRISPR type I-F/YPEST-associated protein Csy2
c: CRISPR-associated endonuclease Cas6/Csy4
d: CRISPR type I-F/YPEST-associated protein Csy3
e: CRISPR type I-F/YPEST-associated protein Csy3
f: CRISPR type I-F/YPEST-associated protein Csy3
g: CRISPR type I-F/YPEST-associated protein Csy3
h: CRISPR type I-F/YPEST-associated protein Csy3
i: CRISPR type I-F/YPEST-associated protein Csy3
m: RNA (61-MER)


Theoretical massNumber of molelcules
Total (without water)780,14222
Polymers780,14222
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
CRISPR-associated ... , 2 types, 4 molecules AaCc

#1: Protein CRISPR-associated protein Csy1


Mass: 49194.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Gene: csy1, PA14_33330 / Production host: Escherichia (bacteria) / References: UniProt: Q02ML9
#3: Protein CRISPR-associated endonuclease Cas6/Csy4


Mass: 21427.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Gene: cas6f, csy4, PA14_33300 / Production host: Escherichia (bacteria)
References: UniProt: Q02MM2, Hydrolases; Acting on ester bonds

-
CRISPR type I-F/YPEST-associated protein ... , 2 types, 14 molecules BbDEFGHIdefghi

#2: Protein CRISPR type I-F/YPEST-associated protein Csy2 / Type I-F CRISPR-associated protein Csy2


Mass: 36244.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria)
Gene: csy2, ALP65_00953, IPC1598_32520, IPC29_26970, PA52Ts2_3638, PACL_0128
Production host: Escherichia (bacteria) / References: UniProt: B3G161
#4: Protein
CRISPR type I-F/YPEST-associated protein Csy3


Mass: 39778.594 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Gene: PA52Ts2_3639 / Production host: Escherichia (bacteria) / References: UniProt: A0A444M080

-
Protein / RNA chain , 2 types, 4 molecules JKMm

#5: Protein AcrIF24


Mass: 24995.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Production host: Escherichia (bacteria)
#6: RNA chain RNA (61-MER)


Mass: 19538.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Production host: Escherichia (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Csy-AcrIF / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 400 kDa/nm / Experimental value: NO
Source (natural)Organism: Pseudomonas (bacteria)
Source (recombinant)Organism: Escherichia (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58133 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 7JZW

7jzw

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00427777
ELECTRON MICROSCOPYf_angle_d0.75938045
ELECTRON MICROSCOPYf_dihedral_angle_d11.5164390
ELECTRON MICROSCOPYf_chiral_restr0.0474280
ELECTRON MICROSCOPYf_plane_restr0.0074785

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more