9P11 | pdb_00009p11

Cas1-Cas2/3 integrase, heterohexameric assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures reveal how the Cas1-2/3 integrase captures, delivers, and integrates foreign DNA into CRISPR loci.

Henriques, W.S.Bowman, J.Hall, L.N.Gauvin, C.C.Wei, H.Kuang, H.Zimanyi, C.M.Eng, E.T.Santiago-Frangos, A.Wiedenheft, B.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.09.007
  • Primary Citation of Related Structures:  
    9P11, 9P1D

  • PubMed Abstract: 

    Cas1 and Cas2 are the hallmark proteins of prokaryotic adaptive immunity. However, these two proteins are often fused to other proteins and the functional association of these fusions often remain poorly understood. Here we purify and determine structures of Cas1 and the Cas2/3 fusion proteins from Pseudomonas aeruginosa at distinct stages of CRISPR adaptation. Collectively, these structures reveal a prominent, positively charged channel on one face of the integration complex that captures short fragments of foreign DNA. Foreign DNA binding triggers conformational changes in Cas2/3 that expose new DNA binding surfaces necessary for homing the DNA-bound integrase to specific CRISPR loci. The length of the foreign DNA substrate determines if Cas1-2/3 docks completely onto the CRISPR repeat to successfully catalyze two sequential transesterification reactions required for integration. Together, these structures clarify how the Cas1-2/3 proteins orchestrate foreign DNA capture, site-specific delivery, and integration of new DNA into the bacterial genome.


  • Organizational Affiliation
    • Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1A [auth F],
B [auth D],
E [auth C],
F [auth E]
324Pseudomonas aeruginosaMutation(s): 0 
Gene Names: cas1PA14_33350
EC: 3.1
UniProt
Find proteins for Q02ML7 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02ML7 
Go to UniProtKB:  Q02ML7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02ML7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPESTC [auth A],
D [auth B]
1,076Pseudomonas aeruginosaMutation(s): 0 
Gene Names: cas3PA14_33340
EC: 3.1 (PDB Primary Data), 3.6.4 (PDB Primary Data)
UniProt
Find proteins for Q02ML8 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02ML8 
Go to UniProtKB:  Q02ML8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02ML8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM134867

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release