9NO4 | pdb_00009no4

Cryo-EM structure of Csm/AcrIIIA2/enolase 3:2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity.

Johnson, K.A.Goswami, H.N.Catchpole, R.J.Ahmadizadeh, F.Zhao, P.Wells, L.Li, H.Terns, M.P.

(2025) Nat Microbiol 10: 3162-3175

  • DOI: https://doi.org/10.1038/s41564-025-02178-2
  • Primary Citation Related Structures: 
    9NO4, 9NQ7

  • PubMed Abstract: 

    CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems provide powerful adaptive immunity against phage infection. In response, phages use anti-CRISPR (Acr) proteins to evade CRISPR immunity. The few type III Acrs identified so far show conditional effectiveness in countering type III immunity or rely on unknown or poorly understood inhibitory mechanisms. Here we report the discovery of AcrIIIA2, a type III-A Acr encoded by Streptococcus thermophilus phages. Biochemical and structural analyses reveal that phage AcrIIIA2 co-opts host enolase, a highly abundant glycolysis enzyme, to form a ternary complex with the S. thermophilus type III-A (Csm) CRISPR ribonucleoprotein complex, obstructing its immune responses. The enolase-chaperoned AcrIIIA2 blocks the initial step of phage RNA binding, thereby preventing downstream type III anti-phage immune responses. Enolase participates in the anti-immune response by serving as an essential structural scaffold, stabilizing Acr-CRISPR interactions. These findings uncover a new anti-defence strategy that exploits a well-conserved host factor to block CRISPR immunity.


  • Organizational Affiliation
    • University of Georgia, Athens, GA, USA.

Macromolecule Content 

  • Total Structure Weight: 665.56 kDa 
  • Atom Count: 46,513 
  • Modeled Residue Count: 5,937 
  • Deposited Residue Count: 5,946 
  • Unique protein chains: 8
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm4A [auth B]299Streptococcus thermophilusMutation(s): 0 
Gene Names: csmcsm4STCNRZ302_04685STHERMO_1022STHERMO_1028STHERMO_1031
UniProt
Find proteins for A0A811IGE5 (Streptococcus thermophilus)
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Go to UniProtKB:  A0A811IGE5
Entity Groups
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UniProt GroupA0A811IGE5
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cms endoribonuclease Csm3B [auth E],
C [auth F]
220Streptococcus thermophilusMutation(s): 0 
Gene Names: csmSTHERMO_1021
UniProt
Find proteins for A0AAN1ZZJ5 (Streptococcus thermophilus)
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UniProt GroupA0AAN1ZZJ5
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cms endoribonuclease Csm3D [auth G]220Streptococcus thermophilusMutation(s): 0 
Gene Names: csmSTHERMO_1021
UniProt
Find proteins for A0AAN1ZZJ5 (Streptococcus thermophilus)
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UniProt GroupA0AAN1ZZJ5
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm2F [auth C],
G [auth D]
130Streptococcus thermophilusMutation(s): 0 
Gene Names: csmSTHERMO_1026
UniProt
Find proteins for A0A8D6U6W4 (Streptococcus thermophilus)
Explore A0A8D6U6W4 
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UniProt GroupA0A8D6U6W4
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm5357Streptococcus thermophilusMutation(s): 0 
Gene Names: csm5
UniProt
Find proteins for A0A0A7HF79 (Streptococcus thermophilus)
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UniProt GroupA0A0A7HF79
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Enolase434Streptococcus thermophilusMutation(s): 0 
Gene Names: enoSTER_0684
EC: 4.2.1.11
UniProt
Find proteins for Q03LI0 (Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9))
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UniProt GroupQ03LI0
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
AcrIIIA2K [auth R]105Streptococcus phage 2972Mutation(s): 0 
Gene Names: CHPC1156_0026
UniProt
Find proteins for A0A3G8FB66 (Streptococcus phage CHPC1156)
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UniProt GroupA0A3G8FB66
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)R [auth A]758Streptococcus thermophilusMutation(s): 0 
Gene Names: cas10csm1
EC: 3.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for A0A0A7HFE1 (Streptococcus thermophilus)
Explore A0A0A7HFE1 
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UniProt GroupA0A0A7HFE1
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
crRNA RNA (35-MER)E [auth N]35Streptococcus thermophilus
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION

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 GM152081

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references