7V02

Staphylococcus epidermidis RP62A CRISPR short effector complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structures of an active type III-A CRISPR effector complex.

Smith, E.M.Ferrell, S.Tokars, V.L.Mondragon, A.

(2022) Structure 30: 1109-1128.e6

  • DOI: https://doi.org/10.1016/j.str.2022.05.013
  • Primary Citation of Related Structures:  
    7UZW, 7UZX, 7UZY, 7UZZ, 7V00, 7V01, 7V02

  • PubMed Abstract: 

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) provide many prokaryotes with an adaptive immune system against invading genetic material. Type III CRISPR systems are unique in that they can degrade both RNA and DNA. In response to invading nucleic acids, they produce cyclic oligoadenylates that act as secondary messengers, activating cellular nucleases that aid in the immune response. Here, we present seven single-particle cryo-EM structures of the type III-A Staphylococcus epidermidis CRISPR effector complex. The structures reveal the intact S. epidermidis effector complex in an apo, ATP-bound, cognate target RNA-bound, and non-cognate target RNA-bound states and illustrate how the effector complex binds and presents crRNA. The complexes bound to target RNA capture the type III-A effector complex in a post-RNA cleavage state. The ATP-bound structures give details about how ATP binds to Cas10 to facilitate cyclic oligoadenylate production.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms endoribonuclease Csm3
A, B, C
214Staphylococcus epidermidis RP62AMutation(s): 0 
UniProt
Find proteins for Q5HK91 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HK91 
Go to UniProtKB:  Q5HK91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HK91
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm5D [auth E]340Staphylococcus epidermidis RP62AMutation(s): 0 
UniProt
Find proteins for Q5HK93 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HK93 
Go to UniProtKB:  Q5HK93
Entity Groups  
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UniProt GroupQ5HK93
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)E [auth F]757Staphylococcus epidermidis RP62AMutation(s): 0 
UniProt
Find proteins for Q5HK89 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HK89 
Go to UniProtKB:  Q5HK89
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UniProt GroupQ5HK89
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm4G [auth H]304Staphylococcus epidermidis RP62AMutation(s): 0 
UniProt
Find proteins for Q5HK92 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HK92 
Go to UniProtKB:  Q5HK92
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UniProt GroupQ5HK92
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm2H [auth I],
I [auth K]
128Staphylococcus epidermidis RP62AMutation(s): 0 
UniProt
Find proteins for Q5HK90 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HK90 
Go to UniProtKB:  Q5HK90
Entity Groups  
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UniProt GroupQ5HK90
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (37-MER)F [auth G]37Staphylococcus epidermidis RP62A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONcryoSPARC

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 StatesR35-GM118108
American Cancer SocietyUnited States134255-PF-20-041-01-DMC
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM129541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM129539

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary