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- EMDB-48771: Cryo-EM Structure of Apo SeAvs7 -

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Basic information

Entry
Database: EMDB / ID: EMD-48771
TitleCryo-EM Structure of Apo SeAvs7
Map data
Sample
  • Complex: Cryo-EM Structure of Apo SeAvs7
    • Protein or peptide: AAA family ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAAA family ATPase / ANTIVIRAL PROTEIN
Function / homologyATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / AAA family ATPase
Function and homology information
Biological speciesHomo sapiens (human) / Salmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsZhang J / Feng L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionJan 23, 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_48771.png

Downloads & links

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Map

FileDownload / File: emd_48771.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 320 pix.
= 302.72 Å		0.95 Å/pix.
x 320 pix.
= 302.72 Å		0.95 Å/pix.
x 320 pix.
= 302.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-9.666777 - 18.033777000000001
Average (Standard dev.)0.0038353412 (±0.1536953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48771_msk_1.map
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Half map: #2

Fileemd_48771_half_map_1.map
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Half map: #1

Fileemd_48771_half_map_2.map
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Sample components

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Entire : Cryo-EM Structure of Apo SeAvs7

EntireName: Cryo-EM Structure of Apo SeAvs7
Components
  • Complex: Cryo-EM Structure of Apo SeAvs7
    • Protein or peptide: AAA family ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM Structure of Apo SeAvs7

SupramoleculeName: Cryo-EM Structure of Apo SeAvs7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 1 / 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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 207066
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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