[English] 日本語
Yorodumi
- PDB-8zlu: Cryo-EM strcuture of Cas5-HNH Cascade,Conf1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zlu
TitleCryo-EM strcuture of Cas5-HNH Cascade,Conf1
Components
  • (CRISPR system Cascade subunit ...) x 2
  • (CRISPR-associated protein ...) x 2
  • CRISPR-associated endoribonuclease Cse3
  • RNA (61-MER)
KeywordsIMMUNE SYSTEM / Cryo-EM strcuture / Cascade / CRISPR-Cas
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA binding / zinc ion binding
Similarity search - Function
CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein ...CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / HNH endonuclease / HNH endonuclease / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / HNH nucleases / CRISPR-associated protein Cas5, N-terminal / HNH nuclease
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR system Cascade subunit CasC / CRISPR-associated endoribonuclease Cse3 / CRISPR system Cascade subunit CasD / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 (CRISPR_cse1)
Similarity search - Component
Biological speciesCandidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsLiu, Y.N. / Wang, L. / Zhang, H. / Zhu, H.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex.
Authors: Yanan Liu / Lin Wang / Qian Zhang / Pengyu Fu / Lingling Zhang / Ying Yu / Heng Zhang / Hongtao Zhu /
Abstract: Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in ...Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in prokaryotes, providing defense against foreign genetic elements. Unlike the previously characterized Cas3 nuclease, which exhibits progressive DNA cleavage in the typical type I-E system, a recently identified HNH-comprising Cascade system enables precise DNA cleavage. Here, we present several near-atomic cryo-electron microscopy (cryo-EM) structures of the Candidatus Cloacimonetes bacterium Cas5-HNH/Cascade complex, both in its DNA-bound and unbound states. Our analysis reveals extensive interactions between the HNH domain and adjacent subunits, including Cas6 and Cas11, with mutations in these key interactions significantly impairing enzymatic activity. Upon DNA binding, the Cas5-HNH/Cascade complex adopts a more compact conformation, with subunits converging toward the center of nuclease, leading to its activation. Notably, we also find that divalent ions such as zinc, cobalt, and nickel down-regulate enzyme activity by destabilizing the Cascade complex. Together, these findings offer structural insights into the assembly and activation of the Cas5-HNH/Cascade complex.
History
DepositionMay 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (61-MER)
C: CRISPR-associated protein Cse1 (CRISPR_cse1)
E: CRISPR-associated protein Cse2 (CRISPR_cse2)
F: CRISPR system Cascade subunit CasC
H: CRISPR system Cascade subunit CasC
I: CRISPR system Cascade subunit CasC
J: CRISPR system Cascade subunit CasC
K: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
B: CRISPR system Cascade subunit CasD
D: CRISPR-associated endoribonuclease Cse3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,79913
Polymers427,75111
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
CRISPR-associated protein ... , 2 types, 2 molecules CE

#2: Protein CRISPR-associated protein Cse1 (CRISPR_cse1)


Mass: 62145.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Gene: BWX75_00747 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V6F8D1
#3: Protein CRISPR-associated protein Cse2 (CRISPR_cse2)


Mass: 20300.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Gene: BWX75_00748 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V6F8C9

-
CRISPR system Cascade subunit ... , 2 types, 7 molecules FHIJKGB

#4: Protein
CRISPR system Cascade subunit CasC


Mass: 41794.367 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Gene: casC, BWX75_00749 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V6F8B5
#5: Protein CRISPR system Cascade subunit CasD


Mass: 43621.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Gene: casD, BWX75_00750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V6F8C5

-
RNA chain / Protein / Non-polymers , 3 types, 4 molecules AD

#1: RNA chain RNA (61-MER)


Mass: 19697.695 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
#6: Protein CRISPR-associated endoribonuclease Cse3


Mass: 31218.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Gene: cse3, BWX75_00751 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1V6F8C4, Hydrolases; Acting on ester bonds
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cas5-HNH Cascade / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 400 kDa/nm / Experimental value: YES
Source (natural)Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 12000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181932 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00227771
ELECTRON MICROSCOPYf_angle_d0.51937952
ELECTRON MICROSCOPYf_dihedral_angle_d10.1714277
ELECTRON MICROSCOPYf_chiral_restr0.044231
ELECTRON MICROSCOPYf_plane_restr0.0044719

+
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