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- PDB-7jhy: Type IV-B CRISPR Complex -

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Basic information

Entry
Database: PDB / ID: 7jhy
TitleType IV-B CRISPR Complex
Components
  • Csf2 (Cas7)
  • Csf4 (Cas11)
  • RNA (31-MER)
KeywordsIMMUNE SYSTEM/RNA / CRISPR Complex / IMMUNE SYSTEM-RNA complex
Function / homologyCRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA / RNA (> 10) / CRISPR type III-associated protein domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium sp. JS623 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBravo, J.P.K. / Taylor, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160088 United States
CitationJournal: iScience / Year: 2021
Title: Structure of a type IV CRISPR-Cas ribonucleoprotein complex.
Authors: Yi Zhou / Jack P K Bravo / Hannah N Taylor / Jurre A Steens / Ryan N Jackson / Raymond H J Staals / David W Taylor /
Abstract: We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector ...We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined with a small subunit (Cas11) filament, but the complex lacks subunits for RNA processing and target DNA cleavage. Surprisingly, instead of assembling around a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of a regular length arranged in a pseudo-A-form configuration. These findings provide a high-resolution glimpse into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture, and suggesting a function for type IV-B RNPs that may be distinct from other class 1 CRISPR-associated systems.
History
DepositionJul 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-22340
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
e: Csf2 (Cas7)
d: Csf2 (Cas7)
c: Csf2 (Cas7)
f: Csf2 (Cas7)
b: Csf2 (Cas7)
a: Csf2 (Cas7)
z: RNA (31-MER)
h: Csf4 (Cas11)
g: Csf4 (Cas11)
j: Csf4 (Cas11)
k: Csf4 (Cas11)
i: Csf4 (Cas11)


Theoretical massNumber of molelcules
Total (without water)291,76912
Polymers291,76912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area32670 Å2
ΔGint-190 kcal/mol
Surface area104890 Å2

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Components

#1: Protein
Csf2 (Cas7)


Mass: 32085.174 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. JS623 (bacteria) / Gene: Mycsm_07113 / Production host: Escherichia coli (E. coli) / References: UniProt: L0J6R6
#2: RNA chain RNA (31-MER)


Mass: 9561.382 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. JS623 (bacteria) / Production host: Escherichia coli (E. coli)
#3: Protein
Csf4 (Cas11)


Mass: 17939.254 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. JS623 (bacteria) / Gene: Mycsm_07114 / Production host: Escherichia coli (E. coli) / References: UniProt: L0JA79
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Csf CRISPR Complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium sp. JS623 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 296319 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00517025
ELECTRON MICROSCOPYf_angle_d1.10423361
ELECTRON MICROSCOPYf_dihedral_angle_d22.1922653
ELECTRON MICROSCOPYf_chiral_restr0.0572766
ELECTRON MICROSCOPYf_plane_restr0.0072942

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