4U7U

Crystal structure of RNA-guided immune Cascade complex from E.coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.003 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli

Zhao, H.Sheng, G.Wang, J.Wang, M.Bunkoczi, G.Gong, W.Wei, Z.Wang, Y.

(2014) Nature 515: 147-150

  • DOI: 10.1038/nature13733

  • PubMed Abstract: 
  • Clustered regularly interspaced short palindromic repeats (CRISPR) together with CRISPR-associated (Cas) proteins form the CRISPR/Cas system to defend against foreign nucleic acids of bacterial and archaeal origin. In the I-E subtype CRISPR/Cas syste ...

    Clustered regularly interspaced short palindromic repeats (CRISPR) together with CRISPR-associated (Cas) proteins form the CRISPR/Cas system to defend against foreign nucleic acids of bacterial and archaeal origin. In the I-E subtype CRISPR/Cas system, eleven subunits from five Cas proteins (CasA1B2C6D1E1) assemble along a CRISPR RNA (crRNA) to form the Cascade complex. Here we report on the 3.05 Å crystal structure of the 405-kilodalton Escherichia coli Cascade complex that provides molecular details beyond those available from earlier lower-resolution cryo-electron microscopy structures. The bound 61-nucleotide crRNA spans the entire 11-protein subunit-containing complex, where it interacts with all six CasC subunits (named CasC1-6), with its 5' and 3' terminal repeats anchored by CasD and CasE, respectively. The crRNA spacer region is positioned along a continuous groove on the concave surface generated by the aligned CasC1-6 subunits. The five long β-hairpins that project from individual CasC2-6 subunits extend across the crRNA, with each β-hairpin inserting into the gap between the last stacked base and its adjacent splayed counterpart, and positioned within the groove of the preceding CasC subunit. Therefore, instead of continuously stacking, the crRNA spacer region is divided into five equal fragments, with each fragment containing five stacked bases flanked by one flipped-out base. Each of those crRNA spacer fragments interacts with CasC in a similar fashion. Furthermore, our structure explains why the seed sequence, with its outward-directed bases, has a critical role in target DNA recognition. In conclusion, our structure of the Cascade complex provides novel molecular details of protein-protein and protein-RNA alignments and interactions required for generation of a complex mediating RNA-guided immune surveillance.


    Organizational Affiliation

    Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Cambridge Institute for Medical Research, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, UK.,Department of Biology, South University of Science and Technology of China, Shenzhen, 518055, China.,1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasA
A, M
502Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casA (cse1, ygcL)
Find proteins for Q46901 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46901
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasB
B, C, N, O
160Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casB (cse2, ygcK)
Find proteins for P76632 (Escherichia coli (strain K12))
Go to UniProtKB:  P76632
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasE
D, P
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casE (cas6e, ygcH)
EC: 3.1.-.-
Find proteins for Q46897 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasC
E, F, G, H, I, J, Q, R, S, T, U, V
363Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casC (cas4, cse4, ygcJ)
Find proteins for Q46899 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46899
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasD
K, W
224Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casD (cas5, ygcI)
Find proteins for Q46898 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46898
Entity ID: 6
MoleculeChainsLengthOrganism
crRNAL,X61Escherichia coli str. K-12 substr. MG1655
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.003 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 111.412α = 92.23
b = 118.143β = 93.55
c = 225.873γ = 106.06
Software Package:
Software NamePurpose
PHASERmodel building
HKLdata scaling
HKL-2000data processing
RESOLVEphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKLdata reduction
PHENIXrefinement
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references