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- EMDB-35121: The asymmetric unit of P22 empty capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-35121
TitleThe asymmetric unit of P22 empty capsid
Map data
Sample
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Major capsid protein
KeywordsComplex / VIRUS / VIRAL PROTEIN
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesSalmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXiao H / Liu HR / Cheng LP
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Viruses / Year: 2023
Title: Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures.
Authors: Hao Xiao / Junquan Zhou / Fan Yang / Zheng Liu / Jingdong Song / Wenyuan Chen / Hongrong Liu / Lingpeng Cheng /
Abstract: The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid ...The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation.
History
DepositionJan 13, 2023-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35121.png

Downloads & links

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Map

FileDownload / File: emd_35121.map.gz / Format: CCP4 / Size: 178 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.)
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.8
Minimum - Maximum-9.346691 - 23.468184000000001
Average (Standard dev.)0.0036700882 (±1.0221509)
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: #2

Fileemd_35121_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_35121_half_map_2.map
Projections & Slices
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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

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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: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 46.795613 KDa
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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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: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 406980
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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