6C66

CRISPR RNA-guided surveillance complex, pre-nicking


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure basis for RNA-guided DNA degradation by Cascade and Cas3.

Xiao, Y.Luo, M.Dolan, A.E.Liao, M.Ke, A.

(2018) Science 361

  • DOI: https://doi.org/10.1126/science.aat0839
  • Primary Citation of Related Structures:  
    6C66

  • PubMed Abstract: 

    Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and the nuclease-helicase fusion enzyme Cas3, respectively. Here, we present a 3.7-angstrom-resolution cryo-electron microscopy (cryo-EM) structure of the Type I-E Cascade/R-loop/Cas3 complex, poised to initiate DNA degradation. Cas3 distinguishes Cascade conformations and only captures the R-loop-forming Cascade, to avoid cleaving partially complementary targets. Its nuclease domain recruits the nontarget strand (NTS) DNA at a bulged region for the nicking of single-stranded DNA. An additional 4.7-angstrom-resolution cryo-EM structure captures the postnicking state, in which the severed NTS retracts to the helicase entrance, to be threaded for adenosine 5'-triphosphate-dependent processive degradation. These snapshots form the basis for understanding RNA-guided DNA degradation in Type I-E CRISPR-Cas systems.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated helicase, Cas3 familyA [auth G]944Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1593
UniProt
Find proteins for Q47PJ0 (Thermobifida fusca (strain YX))
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Go to UniProtKB:  Q47PJ0
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ0
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cse1 familyB [auth A]549Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1592
UniProt
Find proteins for Q47PJ1 (Thermobifida fusca (strain YX))
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Go to UniProtKB:  Q47PJ1
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UniProt GroupQ47PJ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cse4 family373Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1590
UniProt
Find proteins for Q47PJ3 (Thermobifida fusca (strain YX))
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Go to UniProtKB:  Q47PJ3
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UniProt GroupQ47PJ3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
I, K
244Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1591
UniProt
Find proteins for Q47PJ2 (Thermobifida fusca (strain YX))
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Go to UniProtKB:  Q47PJ2
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UniProt GroupQ47PJ2
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cas5e family254Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1589
UniProt
Find proteins for Q47PJ4 (Thermobifida fusca (strain YX))
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UniProt GroupQ47PJ4
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cse3 family232Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1588
UniProt
Find proteins for Q47PJ5 (Thermobifida fusca (strain YX))
Explore Q47PJ5 
Go to UniProtKB:  Q47PJ5
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UniProt GroupQ47PJ5
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
crRNA61Thermobifida fusca
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Entity ID: 6
MoleculeChains LengthOrganismImage
Target strand55Thermobifida fusca
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Entity ID: 8
MoleculeChains LengthOrganismImage
Nontarget strand55Thermobifida fusca
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118174
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102543

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Derived calculations