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- EMDB-73002: Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B -

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Basic information

Entry
Database: EMDB / ID: EMD-73002
TitleCryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B
Map data
Sample
  • Complex: Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B
KeywordsAAA family ATPase / ANTIMICROBIAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.01 Å
AuthorsZhang J / Feng L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: bioRxiv / Year: 2026
Title: Diverse bacterial pattern recognition receptors sense the conserved phage proteome.
Authors: Hyunbin Lee / Sofia Luengo-Woods / Jianxiu Zhang / Kira S Makarova / Yuri I Wolf / Collin Chiu / Simone A Evans / Junyi Chen / Haopeng Xiao / Liang Feng / Eugene V Koonin / Alex Gao /
Abstract: Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs), play a central role in this process. In bacteria and archaea, although several STAND NTPase families have been reported to sense phage proteins, their functional diversity remains largely unexplored. Here, we conducted a systematic phylogenetic analysis of prokaryotic STAND NTPases and identified at least 90 structurally distinct families associated with antiviral defense. We first show that the uncharacterized Avs7 family recognizes the major capsid protein (MCP) of tailed phages. Three cryo-EM structures of Avs7 reveal an asymmetric, butterfly-shaped tetramer that assembles stepwise via large, MCP-induced conformational changes, incorporating bacterial translation elongation factor Tu (EF-Tu) as a scaffold that is required for full defense activity. Using highly parallel genetic screens, we further show that 13 additional STAND families sense 12 conserved phage protein folds, encompassing most of the core structural and replicative components of tailed phages. These include two structurally distinct families-Avs8 (PD-λ-4) and Avs10 (Erebus/Hypnos/bNACHT64)-that also recognize MCP, as well as 11 other families (Avs11-21) that recognize the portal, portal adaptor, tail nozzle, head-tail connector, tail terminator, tail tube protein, tail assembly chaperone, tape measure protein, DNA polymerase, helicase/RecA-type ATPase, and single-stranded DNA annealing protein (SSAP), respectively. Together, our findings highlight structure-based pattern recognition and host factor repurposing as fundamental strategies of bacterial immunity.
History
DepositionOct 2, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73002.png

Downloads & links

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Map

FileDownload / File: emd_73002.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 480 pix.
= 456. Å		0.95 Å/pix.
x 480 pix.
= 456. Å		0.95 Å/pix.
x 480 pix.
= 456. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3931549 - 0.71203387
Average (Standard dev.)0.00024908964 (±0.0063695344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73002_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_73002_half_map_1.map
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Half map: #2

Fileemd_73002_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B

EntireName: Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B
Components
  • Complex: Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B

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Supramolecule #1: Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B

SupramoleculeName: Cryo-EM structure of SeAvs7 MCP EFTu1 monomeric complex-Map B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 78090
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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