6QXF

Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System.

Wilkinson, M.Drabavicius, G.Silanskas, A.Gasiunas, G.Siksnys, V.Wigley, D.B.

(2019) Mol Cell 75: 90-101.e5

  • DOI: https://doi.org/10.1016/j.molcel.2019.04.020
  • Primary Citation of Related Structures:  
    6QXF, 6QXT, 6QY3

  • PubMed Abstract: 

    CRISPR and associated Cas proteins function as an adaptive immune system in prokaryotes to combat bacteriophage infection. During the immunization step, new spacers are acquired by the CRISPR machinery, but the molecular mechanism of spacer capture remains enigmatic. We show that the Cas9, Cas1, Cas2, and Csn2 proteins of a Streptococcus thermophilus type II-A CRISPR-Cas system form a complex and provide cryoelectron microscopy (cryo-EM) structures of three different assemblies. The predominant form, with the stoichiometry Cas1 8 -Cas2 4 -Csn2 8 , referred to as monomer, contains ∼30 bp duplex DNA bound along a central channel. A minor species, termed a dimer, comprises two monomers that sandwich a further eight Cas1 and four Cas2 subunits and contains two DNA ∼30-bp duplexes within the channel. A filamentous form also comprises Cas1 8 -Cas2 4 -Csn2 8 units (typically 2-6) but with a different Cas1-Cas2 interface between them and a continuous DNA duplex running along a central channel.


  • Organizational Affiliation

    Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Csn2
A, B, C, D, E
A, B, C, D, E, F, G, H
219Streptococcus thermophilusMutation(s): 0 
Gene Names: csn2
UniProt
Find proteins for G3ECR4 (Streptococcus thermophilus)
Explore G3ECR4 
Go to UniProtKB:  G3ECR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3ECR4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1
I, J, L, M, O
I, J, L, M, O, P, R, S
302Streptococcus thermophilusMutation(s): 0 
Gene Names: cas1
EC: 3.1
UniProt
Find proteins for G3ECR2 (Streptococcus thermophilus)
Explore G3ECR2 
Go to UniProtKB:  G3ECR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3ECR2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas2
K, N, Q, T
114Streptococcus thermophilusMutation(s): 0 
Gene Names: cas2
EC: 3.1
UniProt
Find proteins for G3ECR3 (Streptococcus thermophilus)
Explore G3ECR3 
Go to UniProtKB:  G3ECR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3ECR3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (25-MER)U [auth X]25Escherichia coli BL21(DE3)
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (25-MER)V [auth Y]25Escherichia coli BL21(DE3)
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTCoot
MODEL REFINEMENTREFMAC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references