4P6I | pdb_00004p6i

Crystal structure of the Cas1-Cas2 complex from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb4P6I/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-24 Released: 2014-05-07 
• Deposition Author(s): Nunez, J.K., Kranzusch, P.J., Noeske, J., Doudna, J.A.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.

Nunez, J.K., Kranzusch, P.J., Noeske, J., Wright, A.V., Davies, C.W., Doudna, J.A.

(2014) Nat Struct Mol Biol 21: 528-534

• PubMed: 24793649 
• DOI: https://doi.org/10.1038/nsmb.2820
• Primary Citation Related Structures: 
  4P6I


• PubMed Abstract: 
  

  The initial stage of CRISPR-Cas immunity involves the integration of foreign DNA spacer segments into the host genomic CRISPR locus. The nucleases Cas1 and Cas2 are the only proteins conserved among all CRISPR-Cas systems, yet the molecular functions of these proteins during immunity are unknown. Here we show that Cas1 and Cas2 from Escherichia coli form a stable complex that is essential for spacer acquisition and determine the 2.3-Å-resolution crystal structure of the Cas1-Cas2 complex. Mutations that perturb Cas1-Cas2 complex formation disrupt CRISPR DNA recognition and spacer acquisition in vivo. Active site mutants of Cas2, unlike those of Cas1, can still acquire new spacers, thus indicating a nonenzymatic role of Cas2 during immunity. These results reveal the universal roles of Cas1 and Cas2 and suggest a mechanism by which Cas1-Cas2 complexes specify sites of CRISPR spacer integration.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, USA.
1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, USA. [3] Department of Chemistry, University of California, Berkeley, Berkeley, California, USA. [4] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 156.05 kDa 
• Atom Count: 10,450 
• Modeled Residue Count: 1,291 
• Deposited Residue Count: 1,426 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cas2	A, B	103	Escherichia coli K-12	Mutation(s): 0  Gene Names: ygbF, cas2, b2754, JW5438 EC: 3.1
UniProt
Find proteins for P45956 (Escherichia coli (strain K12)) Explore P45956  Go to UniProtKB:  P45956

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas1	C, D, E, F	305	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2755, cas1, JW2725, pstS, ygbT EC: 3.1
UniProt
Find proteins for Q46896 (Escherichia coli (strain K12)) Explore Q46896  Go to UniProtKB:  Q46896

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.875	α = 90
b = 125.696	β = 102.74
c = 99.306	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Nunez, J.K., Kranzusch, P.J., Noeske, J., Doudna, J.A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1244557

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2015-01-07
  Changes: Database references
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.5: 2019-11-27
  Changes: Author supporting evidence
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references, Refinement description