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- EMDB-73001: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex -

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Basic information

Entry
Database: EMDB / ID: EMD-73001
TitleCryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex
Map data
Sample
  • Complex: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex
    • Protein or peptide: Major capsid protein
  • Protein or peptide: AAA family ATPase
  • Protein or peptide: Elongation factor Tu 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsAAA family ATPase / ANTIMICROBIAL PROTEIN
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
AAA family ATPase / Major capsid protein / Elongation factor Tu 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Salmonella enterica (bacteria) / Escherichia coli (E. coli) / Escherichia phage ZL19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 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_73001.png

Downloads & links

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Map

FileDownload / File: emd_73001.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-49.601520000000001 - 86.305260000000004
Average (Standard dev.)0.026515266 (±1.2825159)
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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Sample components

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Entire : Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex

EntireName: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex
Components
  • Complex: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex
    • Protein or peptide: Major capsid protein
  • Protein or peptide: AAA family ATPase
  • Protein or peptide: Elongation factor Tu 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of SeAvs7 MCP EFTu1 tetrameric complex

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

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Macromolecule #1: AAA family ATPase

MacromoleculeName: AAA family ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 172.696516 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSIAGIRSNR GDGYQTLVAF DWALTVLSDQ DFQWIEIDSI SYLVDDVVIG KIDGNIIACQ CKKNQTDFKA WTIADLGDEL DKASLLLAE NPKVNVRFYS RNNFGDLAKL KEHSSSQPDE GSYQQSLGKA QRLLDDALSK QLAKIAPSLS TFEFLSRTNF V TSDDLDRM ...String:
MSIAGIRSNR GDGYQTLVAF DWALTVLSDQ DFQWIEIDSI SYLVDDVVIG KIDGNIIACQ CKKNQTDFKA WTIADLGDEL DKASLLLAE NPKVNVRFYS RNNFGDLAKL KEHSSSQPDE GSYQQSLGKA QRLLDDALSK QLAKIAPSLS TFEFLSRTNF V TSDDLDRM EALLRERLRN LVSNTDSAFN ALWMKLDQLG ARMDGSRSST AVQHRLTKHD LRNIIQQSGS TLAPPMDLVG IR HSFSSTS AIGRSWRRDI AGLRITSPIV NEILAAIDVR KRSILLTGLP GSGKTCVMLA LQEALEERVK TCSNIVPLFI QSR EFADLA TSEERQVQGL SQQWVEKAAR LAEDAHVVVV IDSLDVLSIA REHRVLQYFL AQIDRLLLIP NITVVTACRD FDKH YDRRI AERHWDCELK CQPLDWNNEI VPLLDTLGIA TAAIDADTRE LIRNPRELAL FVELARRDGS FNVVTSQALA QRYLD TIVL ADSDLGDNAI QAIEAIASEM LKMRSLVVPH QRFTASPDIQ RKLCSLNVLQ ETQDGKLTFG HQTLLDVLVI SRAIRN GVT LNEFIRGLPP VPFVRPSIRS FIAQLALGER REYRKQLRTV LTGNAAFHIR RLVAESFAEQ KPQNEDWLLI RELREKN RE VFQVVYVAGG SIEWHRFWIN NLVPYLKATR DAEGVAMHVH RIAQWSNIDT AGVVSFWIEA LTLNWFDGNG IADQIAMH L SVIKAENLSV VVPLLMRLLD TPLSDYSPLG EVIANCVAAG VIGDTLLWRY ITDGLTGEDI LQNRFDNKLR CQPHEFGSK NENFLQQRMV QSSALLDLAV EAIEYWSYTQ ESQYGATRIS YRYGFLGETS YENVHSQRDI HHVDSMNILF DAVEAGILYN AKIHSNWWQ KNCERLCFHH EGALLYFGIL ACTQSPEANI DLIGRMLCDR SMLEFELSFE LGGLIRSIFT FLPSPKQDAV M ASILNMWK DVADSNDLRV MKSQAEVIVS IPCHLRSLEA QAVLDTYEKK AGVLIRQPKI HSHGGIVRAP FSFELFLGIN DD GVLKLLA HYEGHSGWDW NDFLVGGERE VGWQLREASS RHPSRFLGLL SNHWTDIPES FRDDVMSGVS TYLAHRYGNL KAD ETWNPL EEPDASLLAN RILDELERHP RYWRHRRSTA KALEACSHVI HDPRKAEQLL FLAIDFVGFQ EEDPIKGDSV GLLG LGLNM AKGAVAEALM ILADNFLAQD NEFPELLAPT LRRFARDKHP AVRAMILRRL PYLQSKSFDF GWDLFHLVMQ DADGL WKIA ERCLYYAYHR HFDVVEPLLA RLRCEGRGKD LETWGRISAL AAMTQHVEFN EFLNDLNALD TTEAWHGATT VWTNAE NMR QQREQCFAGI KAGLNADGRH ALGVAGEMAR IFHYKGEVVF VPIGLLSRCF SVFENAGDGE KKHPRFFGFI EWLNVIS LQ DPEYALAATE IYLAYVDHSK QRLYDHNDNL TQLMTRLFAE AEEREESDRG SMLQRVVAIQ DTLLSLGVKE IADWLKAA E RP

UniProtKB: AAA family ATPase

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Macromolecule #2: Elongation factor Tu 1

MacromoleculeName: Elongation factor Tu 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.340465 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSKEKFERTK PHVNVGTIGH VDHGKTTLTA AITTVLAKTY GGAARAFDQI DNAPEEKARG ITINTSHVEY DTPTRHYAHV DCPGHADYV KNMITGAAQM DGAILVVAAT DGPMPQTREH ILLGRQVGVP YIIVFLNKCD MVDDEELLEL VEMEVRELLS Q YDFPGDDT ...String:
MSKEKFERTK PHVNVGTIGH VDHGKTTLTA AITTVLAKTY GGAARAFDQI DNAPEEKARG ITINTSHVEY DTPTRHYAHV DCPGHADYV KNMITGAAQM DGAILVVAAT DGPMPQTREH ILLGRQVGVP YIIVFLNKCD MVDDEELLEL VEMEVRELLS Q YDFPGDDT PIVRGSALKA LEGDAEWEAK ILELAGFLDS YIPEPERAID KPFLLPIEDV FSISGRGTVV TGRVERGIIK VG EEVEIVG IKETQKSTCT GVEMFRKLLD EGRAGENVGV LLRGIKREEI ERGQVLAKPG TIKPHTKFES EVYILSKDEG GRH TPFFKG YRPQFYFRTT DVTGTIELPE GVEMVMPGDN IKMVVTLIHP IAMDDGLRFA IREGGRTVGA GVVAKVLG

UniProtKB: Elongation factor Tu 1

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Macromolecule #3: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage ZL19 (virus)
Molecular weightTheoretical: 34.455023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAIKFDAEQA KITAHLEQMG VEKADAAGIW TVKQLTATLN RAYEKEYADN SVVNIFPVTN EIPGHAKYFE YPEFDGVGIA QIIADYSDD LPLVDAFMTE KQGKVFRFGN AFLISTDEIK AGAATGQPLS ARKQALAFEA HDNLLDKLVW SGSAPHGIVS V FDQPNINN ...String:
MAIKFDAEQA KITAHLEQMG VEKADAAGIW TVKQLTATLN RAYEKEYADN SVVNIFPVTN EIPGHAKYFE YPEFDGVGIA QIIADYSDD LPLVDAFMTE KQGKVFRFGN AFLISTDEIK AGAATGQPLS ARKQALAFEA HDNLLDKLVW SGSAPHGIVS V FDQPNINN VVATPDWSAP QNAINDVTAM IDAVETSTQG FHHVTDILLP ASARRVMQRL VPNTTLSYGE LFTRNNPGMT IR FMQFLDN YDGAGGKAAL AFEKDPLNMS IEIPEVTNVL PAQPKDLHFR YPVTSKATGL IVYRPLTMAV IKGITFA

UniProtKB: Major capsid protein

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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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: 3.43 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

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