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- EMDB-71631: Cryo-EM structure of bacteriophage P22 gp1-gp5-gp4 complex at 2.7... -

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Basic information

Entry
Database: EMDB / ID: EMD-71631
TitleCryo-EM structure of bacteriophage P22 gp1-gp5-gp4 complex at 2.76 angstrom
Map datastructure of bacteriophage P22 gp1-gp5-gp4 complex
Sample
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Peptidoglycan hydrolase gp4
    • Protein or peptide: Portal protein
KeywordsPhage capsid-tail interface / VIRAL PROTEIN
Function / homology
Function and homology information


viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral procapsid / viral portal complex / viral procapsid maturation / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail / T=7 icosahedral viral capsid ...viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral procapsid / viral portal complex / viral procapsid maturation / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail / T=7 icosahedral viral capsid / virion assembly / viral capsid / hydrolase activity / identical protein binding
Similarity search - Function
Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5
Similarity search - Domain/homology
Portal protein / Head-to-tail adapter protein gp4 / Major capsid protein
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsYu H / Liu J / Molienux IJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110243 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Structural Basis for Bacteriophage P22 Assembly and Infection Initiation.
Authors: Chunyan Wang / Huaxin Yu / Taehyun Park / Ian J Molineux / Jun Liu /
Abstract: Salmonella phage P22 deploys a highly coordinated tail machine to recognize hosts and initiate infection. Here, we present a cryo-EM structure of wild-type P22 that defines how the tail apparatus ...Salmonella phage P22 deploys a highly coordinated tail machine to recognize hosts and initiate infection. Here, we present a cryo-EM structure of wild-type P22 that defines how the tail apparatus assembles onto the capsid and how they interface. Flexible loop residues on both the portal protein gp1 and the capsid protein gp5 undergo pronounced positional shifts and engage multiple partners to accommodate the C12-C5 symmetry mismatch at the portal-capsid interface. The portal protein gp1 forms a distinctive ∼15-nm barrel that projects deep into the capsid interior. Comparison with a mutant lacking the three internal E (ejection) proteins indicates that these proteins reside within the portal-tail lumen in a poorly ordered state, yet are essential for stabilizing the extended portal barrel. We further show how the hub protein gp10 orchestrates the assembly of four distinct particle isomers through its coordinated interactions with portal gp1, adaptor gp4, tailspike gp9, and needle gp26. Finally, cryo-electron tomography reveals that the gp10 hub acts as a structural foundation for the assembly of one E protein into an extracellular channel that breaches the cell surface, with other E proteins forming a genome-translocating trans-envelope conduit.
History
DepositionJul 7, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71631.png

Downloads & links

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Map

FileDownload / File: emd_71631.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of bacteriophage P22 gp1-gp5-gp4 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0050184047 - 1.9157673
Average (Standard dev.)0.0051571815 (±0.052666012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_71631_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71631_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salmonella phage P22

EntireName: Salmonella phage P22 (virus)
Components
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Peptidoglycan hydrolase gp4
    • Protein or peptide: Portal protein

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Supramolecule #1: Salmonella phage P22

SupramoleculeName: Salmonella phage P22 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2908168 / Sci species name: Salmonella phage P22 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica (bacteria)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 46.795613 KDa
Recombinant expressionOrganism: Salmonella enterica (bacteria)
SequenceString: MALNEGQIVT LAVDEIIETI SAITPMAQKA KKYTPPAASM QRSSNTIWMP VEQESPTQEG WDLTDKATGL LELNVAVNMG EPDNDFFQL RADDLRDETA YRRRIQSAAR KLANNVELKV ANMAAEMGSL VITSPDAIGT NTADAWNFVA DAEEIMFSRE L NRDMGTSY ...String:
MALNEGQIVT LAVDEIIETI SAITPMAQKA KKYTPPAASM QRSSNTIWMP VEQESPTQEG WDLTDKATGL LELNVAVNMG EPDNDFFQL RADDLRDETA YRRRIQSAAR KLANNVELKV ANMAAEMGSL VITSPDAIGT NTADAWNFVA DAEEIMFSRE L NRDMGTSY FFNPQDYKKA GYDLTKRDIF GRIPEEAYRD GTIQRQVAGF DDVLRSPKLP VLTKSTATGI TVSGAQSFKP VA WQLDNDG NKVNVDNRFA TVTLSATTGM KRGDKISFAG VKFLGQMAKN VLAQDATFSV VRVVDGTHVE ITPKPVALDD VSL SPEQRA YANVNTSLAD AMAVNILNVK DARTNVFWAD DAIRIVSQPI PANHELFAGM KTTSFSIPDV GLNGIFATQG DIST LSGLC RIALWYGVNA TRPEAIGVGL PGQTA

UniProtKB: Major capsid protein

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Macromolecule #2: Peptidoglycan hydrolase gp4

MacromoleculeName: Peptidoglycan hydrolase gp4 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 18.044959 KDa
Recombinant expressionOrganism: Salmonella enterica (bacteria)
SequenceString:
MQIKTKGDLV RAALRKLGVA SDATLTDVEP QSMQDAVDDL EAMMAEWYQD GKGIITGYVF SDDENPPAEG DDHGLRSSAV SAVFHNLAC RIAPDYALEA TAKIIATAKY GKELLYKQTA ISRAKRAPYP SRMPTGSGNS FANLNEWHYF PGEQNADSTT P HDEGNG

UniProtKB: Head-to-tail adapter protein gp4

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Macromolecule #3: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 82.829375 KDa
Recombinant expressionOrganism: Salmonella enterica (bacteria)
SequenceString: MADNENRLES ILSRFDADWT ASDEARREAK NDLFFSRVSQ WDDWLSQYTT LQYRGQFDVV RPVVRKLVSE MRQNPIDVLY RPKDGARPD AADVLMGMYR TDMRHNTAKI AVNIAVREQI EAGVGAWRLV TDYEDQSPTS NNQVIRREPI HSACSHVIWD S NSKLMDKS ...String:
MADNENRLES ILSRFDADWT ASDEARREAK NDLFFSRVSQ WDDWLSQYTT LQYRGQFDVV RPVVRKLVSE MRQNPIDVLY RPKDGARPD AADVLMGMYR TDMRHNTAKI AVNIAVREQI EAGVGAWRLV TDYEDQSPTS NNQVIRREPI HSACSHVIWD S NSKLMDKS DARHCTVIHS MSQNGWEDFA EKYDLDADDI PSFQNPNDWV FPWLTQDTIQ IAEFYEVVEK KETAFIYQDP VT GEPVSYF KRDIKDVIDD LADSGFIKIA ERQIKRRRVY KSIITCTAVL KDKQLIAGEH IPIVPVFGEW GFVEDKEVYE GVV RLTKDG QRLRNMIMSF NADIVARTPK KKPFFWPEQI AGFEHMYDGN DDYPYYLLNR TDENSGDLPT QPLAYYENPE VPQA NAYML EAATSAVKEV ATLGVDTEAV NGGQVAFDTV NQLNMRADLE TYVFQDNLAT AMRRDGEIYQ SIVNDIYDVP RNVTI TLED GSEKDVQLMA EVVDLATGEK QVLNDIRGRY ECYTDVGPSF QSMKQQNRAE ILELLGKTPQ GTPEYQLLLL QYFTLL DGK GVEMMRDYAN KQLIQMGVKK PETPEEQQWL VEAQQAKQGQ QDPAMVQAQG VLLQGQAELA KAQNQTLSLQ IDAAKVE AQ NQLNAARIAE IFNNMDLSKQ SEFREFLKTV ASFQQDRSED ARANAELLLK GDEQTHKQRM DIANILQSQR QNQPSGSV A ETPQ

UniProtKB: Portal protein

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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 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 177125
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93834
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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