4U7U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasA
A, M
502Escherichia coli K-12Mutation(s): 0 
Gene Names: casAcse1ygcLb2760JW2730
Find proteins for Q46901 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46901
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasB
B, C, N, O
160Escherichia coli K-12Mutation(s): 0 
Gene Names: casBcse2ygcKb2759JW2729
Find proteins for P76632 (Escherichia coli (strain K12))
Go to UniProtKB:  P76632
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasE
D, P
201Escherichia coli K-12Mutation(s): 0 
Gene Names: casEcas6eygcHb2756JW2726
EC: 3.1
Find proteins for Q46897 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46897
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasC
E, F, G, H, I, J, Q, R, S, T, U, V
363Escherichia coli K-12Mutation(s): 0 
Gene Names: casCcas4cse4ygcJb2758JW2728
Find proteins for Q46899 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46899
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasD
K, W
224Escherichia coli K-12Mutation(s): 0 
Gene Names: casDcas5ygcIb2757JW5844
Find proteins for Q46898 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46898
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
crRNAL, X61Escherichia coli str. K-12 substr. MG1655
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • 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
HKL-2000data processing
HKL-2000data scaling
RESOLVEphasing
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing
PHASERmodel building
HKLdata reduction
HKLdata scaling
PHENIXrefinement

Structure Validation

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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
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy