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- EMDB-61460: P22 procapsid portal -

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Basic information

Entry
Database: EMDB / ID: EMD-61460
TitleP22 procapsid portal
Map data
Sample
  • Complex: Salmonella enterica subsp. enterica serovar Typhimurium
    • Protein or peptide: Portal protein
KeywordsComplex / VIRAL PROTEIN
Function / homologyPhage P22-like portal protein / Phage P22-like portal protein / Portal protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu HR / Xiao H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: PLoS Biol / Year: 2025
Title: Structure of the scaffolding protein and portal within the bacteriophage P22 procapsid provides insights into the self-assembly process.
Authors: Hao Xiao / Wenyuan Chen / Hao Pang / Jing Zheng / Li Wang / Hao Feng / Jingdong Song / Lingpeng Cheng / Hongrong Liu /
Abstract: In the assembly pathway of tailed double-stranded DNA (dsDNA) bacteriophages and herpesviruses, a procapsid with a dodecameric portal for DNA delivery at a unique vertex is initially formed. ...In the assembly pathway of tailed double-stranded DNA (dsDNA) bacteriophages and herpesviruses, a procapsid with a dodecameric portal for DNA delivery at a unique vertex is initially formed. Appropriate procapsid assembly requires the transient presence of multiple copies of a scaffolding protein (SP), which is absent in the mature virion. However, how the SP contributes to dodecameric portal formation, facilitates portal and coat protein incorporation, and is subsequently released remains unclear because of a lack of structural information. Here, we present the structure of the SP-portal complex within the procapsid of bacteriophage P22 at 3-9 Å resolutions. The AlphaFold2-predicted SP model fits well with the density map of the complex. The SP forms trimers and tetramers that interact to yield a dome-like complex on the portal. Two SP domains mediate multimerization. Each trimer interacts with two neighboring portal subunits. The SP has a loop-hook-like structure that aids in coat protein recruitment during viral assembly. The loops of those SP subunits on the portal are positioned in clefts between adjacent portal subunits. Conformational changes in the portal during phage maturation may trigger the disassembly and release of the SP complex. Our findings provide insights into SP-assisted procapsid assembly in bacteriophage P22 and suggest that this strategy is also implemented by other dsDNA viruses, including herpesviruses.
History
DepositionSep 6, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61460.png

Downloads & links

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Map

FileDownload / File: emd_61460.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6
Minimum - Maximum-10.584379999999999 - 16.850197000000001
Average (Standard dev.)0.010471686 (±0.8827473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61460_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61460_half_map_2.map
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 enterica subsp. enterica serovar Typhimurium

EntireName: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Components
  • Complex: Salmonella enterica subsp. enterica serovar Typhimurium
    • Protein or peptide: Portal protein

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Supramolecule #1: Salmonella enterica subsp. enterica serovar Typhimurium

SupramoleculeName: Salmonella enterica subsp. enterica serovar Typhimurium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 82.829375 KDa
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22169
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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