4QTS

Crystal structure of Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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Literature

Crystal Structure of the Csm3-Csm4 Subcomplex in the Type III-A CRISPR-Cas Interference Complex.

Numata, T.Inanaga, H.Sato, C.Osawa, T.

(2014) J Mol Biol 

  • DOI: 10.1016/j.jmb.2014.09.029
  • Primary Citation of Related Structures:  
    4QTS

  • PubMed Abstract: 
  • Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation ...

    Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3-Csm4 subcomplex at 3.1Å resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1-Csm4-Csm3 ternary complex, which provides insights into its role in the Csm interference complex.


    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR type III-associated RAMP protein Csm4A, B376Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: csm4MJ1668
UniProt
Find proteins for Q59062 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q59062 
Go to UniProtKB:  Q59062
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR type III-associated RAMP protein Csm3C, D268Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: csm3MJ1669
EC: 3.1
UniProt
Find proteins for Q59063 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q59063 
Go to UniProtKB:  Q59063
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth C], F [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.653α = 90
b = 96.319β = 90
c = 194.797γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SHARPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release