6SHB

Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP, state 1, in the presence of ssDNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas.

Sofos, N.Feng, M.Stella, S.Pape, T.Fuglsang, A.Lin, J.Huang, Q.Li, Y.She, Q.Montoya, G.

(2020) Mol Cell 79: 741-757.e7

  • DOI: https://doi.org/10.1016/j.molcel.2020.07.008
  • Primary Citation of Related Structures:  
    6S6B, 6S8B, 6S8E, 6S91, 6SH8, 6SHB, 6SIC

  • PubMed Abstract: 

    Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific single-stranded RNA (ssRNA) hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-β, unveiling how binding of the target RNA regulates the Cmr2 activities. Cryoelectron microscopy (cryo-EM) analysis revealed the unique subunit architecture of Cmr-β and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA-bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5' tag in the CRISPR RNAs (crRNA) and the 3' antitag of the target RNA activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self- versus non-self-recognition. These findings highlight the diverse defense strategies of type III complexes.


  • Organizational Affiliation

    Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cmr5 family
A, B, C
155Sulfolobus islandicus REY15AMutation(s): 0 
UniProt
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UniProt GroupF0NDX5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated RAMP protein, Cmr4 family
D, E, F, G
286Sulfolobus islandicus REY15AMutation(s): 1 
Gene Names: SiRe_0602
UniProt
Find proteins for F0NDX6 (Sulfolobus islandicus (strain REY15A))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated RAMP protein, Cmr6 familyH [auth I]296Sulfolobus islandicus REY15AMutation(s): 0 
Gene Names: SiRe_0599
UniProt
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UniProt GroupF0NDX3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cmr1,CRISPR-associated RAMP protein, Cmr1 familyI [auth J]476Sulfolobus islandicus REY15AMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Cmrx174Sulfolobus islandicus REY15AMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cmr2 familyHA [auth K]1,037Sulfolobus islandicus REY15AMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Cmr3 familyKA [auth H]313Sulfolobus islandicus REY15AMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains LengthOrganismImage
Cognate target RNA (43-MER)J [auth U]46synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
crRNA (49-MER)K [auth V]51Sulfolobus islandicus REY15A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcisTEM1.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF14CC0001
Novo Nordisk FoundationDenmarkNNF0024386
Novo Nordisk FoundationDenmarkNNF17SA0030214

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-09-16
    Changes: Database references