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- EMDB-49643: Focused map of Csm/AcrIIIA2/enolase 4:3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49643
TitleFocused map of Csm/AcrIIIA2/enolase 4:3 complex
Map dataFocused map of Csm/AcrIIIA2/ enolase complex
Sample
  • Complex: Ternary complex of Csm/AcrIIIA2/enolase 4:3 complex
KeywordsType III-A CRISPR-Cas / Anti-CRISPR / cryo-EM / RNA BINDING PROTEIN
Biological speciesStreptococcus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 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
DepositionMar 11, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49643.png

Downloads & links

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Map

FileDownload / File: emd_49643.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of Csm/AcrIIIA2/ enolase 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: 0.255
Minimum - Maximum-0.9216857 - 1.920383
Average (Standard dev.)-0.0003614023 (±0.031038132)
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 A

Fileemd_49643_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_49643_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of Csm/AcrIIIA2/enolase 4:3 complex

EntireName: Ternary complex of Csm/AcrIIIA2/enolase 4:3 complex
Components
  • Complex: Ternary complex of Csm/AcrIIIA2/enolase 4:3 complex

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Supramolecule #1: Ternary complex of Csm/AcrIIIA2/enolase 4:3 complex

SupramoleculeName: Ternary complex of Csm/AcrIIIA2/enolase 4:3 complex / type: complex / ID: 1 / Parent: 0
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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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 AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325120
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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