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- EMDB-72559: Consensus map of Csm/AcrIIIA2/enolase 3:2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-72559
TitleConsensus map of Csm/AcrIIIA2/enolase 3:2 complex
Map dataconsensus map of Csm/AcrIIIA2/Enolase 3:2 complex
Sample
  • Complex: Csm/AcrIIIA2/enolase complex
Keywordsanti-CRISPR / type III CRISPR / Cryo-EM / structural biology / antibacterial / RNA BINDING PROTEIN
Biological speciesStreptococcus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsGoswami HN / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR000347 United States
CitationJournal: Nat Microbiol / Year: 2025
Title: A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity.
Authors: Katie A Johnson / Hemant N Goswami / Ryan J Catchpole / Fozieh Ahmadizadeh / Peng Zhao / Lance Wells / Hong Li / Michael P Terns /
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 (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.
History
DepositionSep 8, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72559.png

Downloads & links

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Map

FileDownload / File: emd_72559.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map of Csm/AcrIIIA2/Enolase 3:2 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 560 pix.
= 463.68 Å		0.83 Å/pix.
x 560 pix.
= 463.68 Å		0.83 Å/pix.
x 560 pix.
= 463.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.7992447 - 1.5396131
Average (Standard dev.)-0.0004138591 (±0.03192949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 463.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of Csm/AcrIIIA2/Enolase 3:2 complex

Fileemd_72559_half_map_1.map
AnnotationHalf map of Csm/AcrIIIA2/Enolase 3:2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Csm/AcrIIIA2/Enolase 3:2 complex

Fileemd_72559_half_map_2.map
AnnotationHalf map of Csm/AcrIIIA2/Enolase 3:2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Csm/AcrIIIA2/enolase complex

EntireName: Csm/AcrIIIA2/enolase complex
Components
  • Complex: Csm/AcrIIIA2/enolase complex

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Supramolecule #1: Csm/AcrIIIA2/enolase complex

SupramoleculeName: Csm/AcrIIIA2/enolase complex / type: complex / ID: 1 / Parent: 0
Details: AcrIIIA2 forms a stable ternary complex with the type III-A (Csm) crRNP (CRISPR RNA-Protein complex) and host enolase.
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Molecular weightTheoretical: 680 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5 / Component - Concentration: 250.0 mM / Component - Formula: NaCl / Component - Name: Sodium Chloride / Details: 250mM NaCl, 30mM HEPES, 10mM Beta-mercaptoethanol
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4) / Number images used: 311708
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE

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