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 
  • R-Value Observed: 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:  
    5H9E, 5H9F

  • 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 been used to control gene expression and cell fate ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasAA502Escherichia coli K-12Mutation(s): 0 
Gene Names: casAcse1ygcLb2760JW2730
UniProt
Find proteins for Q46901 (Escherichia coli (strain K12))
Explore Q46901 
Go to UniProtKB:  Q46901
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasBB, C165Escherichia coli K-12Mutation(s): 0 
Gene Names: casBcse2ygcKb2759JW2729
UniProt
Find proteins for P76632 (Escherichia coli (strain K12))
Explore P76632 
Go to UniProtKB:  P76632
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasCD, E, F, G, H, I363Escherichia coli K-12Mutation(s): 0 
Gene Names: casCcas4cse4ygcJb2758JW2728
UniProt
Find proteins for Q46899 (Escherichia coli (strain K12))
Explore Q46899 
Go to UniProtKB:  Q46899
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasDJ224Escherichia coli K-12Mutation(s): 0 
Gene Names: casDcas5ygcIb2757JW5844
UniProt
Find proteins for Q46898 (Escherichia coli (strain K12))
Explore Q46898 
Go to UniProtKB:  Q46898
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasEN [auth K]199Escherichia coli K-12Mutation(s): 0 
Gene Names: casEcas6eygcHb2756JW2726
EC: 3.1
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12))
Explore Q46897 
Go to UniProtKB:  Q46897
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
crRNA (61-MER)K [auth L]61Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (28-MER) Non-targetL [auth M]28Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (50-MER) TargetM [auth N]50Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
O [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.979α = 90
b = 150.059β = 90
c = 400.546γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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