5U07

CRISPR RNA-guided surveillance complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

Xiao, Y., Luo, M., Hayes, R.P., Kim, J., Ng, S., Ding, F., Liao, M., Ke, A.

(2017) Cell 170: 48-60.e11

  • DOI: 10.1016/j.cell.2017.06.012
  • Primary Citation of Related Structures:  
    5U07, 5U0A

  • PubMed Abstract: 

    • Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop ...

    Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems.

    Organizational Affiliation: 

    Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA. Electronic address: ailong.ke@cornell.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein, Cse3 familyA232Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1588
UniProt
Find proteins for Q47PJ5 (Thermobifida fusca (strain YX))
Explore Q47PJ5 
Go to UniProtKB:  Q47PJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cse2B, J244Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1591
UniProt
Find proteins for Q47PJ2 (Thermobifida fusca (strain YX))
Explore Q47PJ2 
Go to UniProtKB:  Q47PJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein, Cse1 familyC549Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1592
UniProt
Find proteins for Q47PJ1 (Thermobifida fusca (strain YX))
Explore Q47PJ1 
Go to UniProtKB:  Q47PJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein, Cse4 family
D, E, F, G, H, I
D, E, F, G, H, I
373Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1590
UniProt
Find proteins for Q47PJ3 (Thermobifida fusca (strain YX))
Explore Q47PJ3 
Go to UniProtKB:  Q47PJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein, Cas5e familyM [auth N]254Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1589
UniProt
Find proteins for Q47PJ4 (Thermobifida fusca (strain YX))
Explore Q47PJ4 
Go to UniProtKB:  Q47PJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ4
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
crRNAK 61Thermobifida fusca YX
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
Target StrandL [auth M]21Thermobifida fusca YX
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 8
MoleculeChainsLengthOrganismImage
Nontarget StrandN [auth O]13Thermobifida fusca YX
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other, Structure summary