5H9F

Crystal structure of E. coli Cascade bound to a PAM-containing dsDNA target at 2.45 angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli.

Hayes, R.P.Xiao, Y.Ding, F.van Erp, P.B.Rajashankar, K.Bailey, S.Wiedenheft, B.Ke, A.

(2016) Nature 530: 499-503

  • DOI: 10.1038/nature16995
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clustered regularly interspaced short palindromic repeats (CRISPRs) and the cas (CRISPR-associated) operon form an RNA-based adaptive immune system against foreign genetic elements in prokaryotes. Type I accounts for 95% of CRISPR systems, and has be ...

    Clustered regularly interspaced short palindromic repeats (CRISPRs) and the cas (CRISPR-associated) operon form an RNA-based adaptive immune system against foreign genetic elements in prokaryotes. Type I accounts for 95% of CRISPR systems, and has been used to control gene expression and cell fate. During CRISPR RNA (crRNA)-guided interference, Cascade (CRISPR-associated complex for antiviral defence) facilitates the crRNA-guided invasion of double-stranded DNA for complementary base-pairing with the target DNA strand while displacing the non-target strand, forming an R-loop. Cas3, which has nuclease and helicase activities, is subsequently recruited to degrade two DNA strands. A protospacer adjacent motif (PAM) sequence flanking target DNA is crucial for self versus foreign discrimination. Here we present the 2.45 Å crystal structure of Escherichia coli Cascade bound to a foreign double-stranded DNA target. The 5'-ATG PAM is recognized in duplex form, from the minor groove side, by three structural features in the Cascade Cse1 subunit. The promiscuity inherent to minor groove DNA recognition rationalizes the observation that a single Cascade complex can respond to several distinct PAM sequences. Optimal PAM recognition coincides with wedge insertion, initiating directional target DNA strand unwinding to allow segmented base-pairing with crRNA. The non-target strand is guided along a parallel path 25 Å apart, and the R-loop structure is further stabilized by locking this strand behind the Cse2 dimer. These observations provide the structural basis for understanding the PAM-dependent directional R-loop formation process.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasA
A
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
165Escherichia 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 CasC
D, E, F, G, H, I
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: 4
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasD
J
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: 8
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasE
K
199Escherichia 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: 5
MoleculeChainsLengthOrganism
crRNA (61-MER)L61Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (28-MER) Non-targetM28Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (50-MER) TargetN50Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
23G
Query on 23G
L
RNA OH 3 prime terminusC10 H13 N5 O10 P2G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.979α = 90.00
b = 150.059β = 90.00
c = 400.546γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Database references
  • Version 1.2: 2016-03-09
    Type: Database references