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- PDB-9yix: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex -

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Basic information

Entry
Database: PDB / ID: 9yix
TitleCryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex
Components
  • AAA family ATPase
  • Elongation factor Tu 1
  • Major capsid protein
KeywordsANTIMICROBIAL PROTEIN / AAA family ATPase
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / magnesium ion binding / ATP hydrolysis activity ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / magnesium ion binding / ATP hydrolysis activity / RNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Protein of unknown function DUF2184 / Major capsid protein / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Elongation factor Tu C-terminal domain / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site ...Protein of unknown function DUF2184 / Major capsid protein / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Elongation factor Tu C-terminal domain / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / AAA family ATPase / Major capsid protein / Elongation factor Tu 1
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
Escherichia coli (E. coli)
Escherichia phage ZL19 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsZhang, J. / Feng, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nature / Year: 2026
Title: Diverse bacterial pattern recognition receptors sense the core 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 across all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic NOD-like receptors, play a central ...Recognition of foreign molecules inside cells is critical for immunity across all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic NOD-like receptors, play a central role in this process. In bacteria and archaea, although several STAND families sense phage proteins, their functional diversity remains largely unexplored. Here we conduct a systematic phylogenetic analysis of prokaryotic STAND NTPases and identify at least 90 structurally distinct families associated with antiviral defence. We first show that the uncharacterized Avs7 family recognizes the major capsid protein (MCP) of tailed phages. Three cryogenic electron microscopy structures of Salmonella enterica Avs7 reveal an asymmetric, butterfly-shaped tetramer that assembles stepwise through large, MCP-induced conformational changes, incorporating bacterial elongation factor Tu (EF-Tu) as a structural component that enhances defence. Using genetic screens with a library of 687 phage genes, we further show that 13 additional STAND families sense 13 conserved phage proteins, encompassing most of the core structural and replicative components of tailed phages. These include 2 distinct MCP-sensing families (Avs8 and Avs10) and 11 others (Avs11-21), which 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, respectively. Together, our findings reveal a mechanism of host-factor repurposing and establish structure-based pattern recognition as a fundamental strategy of bacterial immunity.
#1: Journal: 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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AAA family ATPase
G: AAA family ATPase
D: AAA family ATPase
J: AAA family ATPase
I: Elongation factor Tu 1
H: Major capsid protein
C: Elongation factor Tu 1
B: Major capsid protein
F: Elongation factor Tu 1
E: Major capsid protein
L: Elongation factor Tu 1
K: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,006,18724
Polymers1,001,96812
Non-polymers4,21912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 12 molecules AGDJICFLHBEK

#1: Protein
AAA family ATPase


Mass: 172696.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: DUC28_22665 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5H7DAD8
#2: Protein
Elongation factor Tu 1 / EF-Tu 1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit III / P-43


Mass: 43340.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tufA, b3339, JW3301 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CE47
#3: Protein
Major capsid protein


Mass: 34455.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage ZL19 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): 469008 / References: UniProt: A0A9E6YYI9

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex
Type: COMPLEX / Entity ID: #3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Salmonella enterica (bacteria)28901
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78090 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00769274
ELECTRON MICROSCOPYf_angle_d0.85694002
ELECTRON MICROSCOPYf_dihedral_angle_d10.2979401
ELECTRON MICROSCOPYf_chiral_restr0.05310520
ELECTRON MICROSCOPYf_plane_restr0.00712210

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