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 

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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: https://doi.org/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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasA502Escherichia coli K-12Mutation(s): 0 
Gene Names: casA, cse1, ygcL, b2760, JW2730
UniProt
Find proteins for Q46901 (Escherichia coli (strain K12))
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UniProt GroupQ46901
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasB
B, C
165Escherichia coli K-12Mutation(s): 0 
Gene Names: casB, cse2, ygcK, b2759, JW2729
UniProt
Find proteins for P76632 (Escherichia coli (strain K12))
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UniProt GroupP76632
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasC
D, E, F, G, H
D, E, F, G, H, I
363Escherichia coli K-12Mutation(s): 0 
Gene Names: casC, cas4, cse4, ygcJ, b2758, JW2728
UniProt
Find proteins for Q46899 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasD224Escherichia coli K-12Mutation(s): 0 
Gene Names: casD, cas5, ygcI, b2757, JW5844
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasEN [auth K]199Escherichia coli K-12Mutation(s): 0 
Gene Names: casE, cas6e, ygcH, b2756, JW2726
EC: 3.1
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsLengthOrganismImage
crRNA (61-MER)K [auth L]61Escherichia coli
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (28-MER) Non-targetL [auth M]28Escherichia coli
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (50-MER) TargetM [auth N]50Escherichia coli
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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

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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