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- EMDB-34539: Capsid structure of Ralstonia phage GP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-34539
TitleCapsid structure of Ralstonia phage GP4
Map datacapsid
Sample
  • Virus: Ralstonia phage GP4 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Virion associated protein
KeywordsRalstonia phage GP4 / Complex / VIRUS
Function / homologyProtein of unknown function DUF4043 / Phage capsid protein / Virion associated protein / Major capsid protein
Function and homology information
Biological speciesRalstonia phage GP4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLiu HR / Chen WY
Funding support China, 4 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)32200994 China
National Natural Science Foundation of China (NSFC)31971122 China
CitationJournal: Viruses / Year: 2022
Title: A Capsid Structure of   GP4 with a Triangulation Number T = 9.
Authors: Jing Zheng / Wenyuan Chen / Hao Xiao / Fan Yang / Xiaowu Li / Jingdong Song / Lingpeng Cheng / Hongrong Liu /
Abstract: GP4, a new phage, is a short-tailed phage. Few structures of phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo- ...GP4, a new phage, is a short-tailed phage. Few structures of phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between and corresponding phages.
History
DepositionOct 22, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34539.png

Downloads & links

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Map

FileDownload / File: emd_34539.map.gz / Format: CCP4 / Size: 926.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 624 pix.
= 792.48 Å		1.27 Å/pix.
x 624 pix.
= 792.48 Å		1.27 Å/pix.
x 624 pix.
= 792.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 20.0
Minimum - Maximum-125.609830000000002 - 209.969539999999995
Average (Standard dev.)1.2941331 (±14.917944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-312-312-312
Dimensions624624624
Spacing624624624
CellA=B=C: 792.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_34539_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_34539_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ralstonia phage GP4

EntireName: Ralstonia phage GP4 (virus)
Components
  • Virus: Ralstonia phage GP4 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Virion associated protein

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Supramolecule #1: Ralstonia phage GP4

SupramoleculeName: Ralstonia phage GP4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2282904 / Sci species name: Ralstonia phage GP4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 40.819551 KDa
SequenceString: MSSTVIAFGD PKAQKKWSSE LAVDIRKKSY FESRFIGTSE NAVIQRKTEV ESDAGDRVSF DLSVRLRGQP TFGDDRVEGK EENLKFYTD EVIIDQVRHS VSAGGRMSRK RTAHDLRKTG RDRLGDYFYQ LTDELFFMYL SGARGINKDF ILPTSFTGYA K NPFNTPDA ...String:
MSSTVIAFGD PKAQKKWSSE LAVDIRKKSY FESRFIGTSE NAVIQRKTEV ESDAGDRVSF DLSVRLRGQP TFGDDRVEGK EENLKFYTD EVIIDQVRHS VSAGGRMSRK RTAHDLRKTG RDRLGDYFYQ LTDELFFMYL SGARGINKDF ILPTSFTGYA K NPFNTPDA AHLLYGGVAT SKASLANTDT MSRVVIERAN VQATMMQAQD PETANMVPVS VEGEDRYVCV MSPFQEHSLR TS DAAGWLE IQKAAAAAEG RNNPIFKGGL GMIGNTVLHS HRNVVRFSDY GAGSDQPAAR ALFMGRQAAV VAYGTKGGLR YDW QEETKD YGNEPTVASG FIAGIKKTRF NDRDFGVISI DTYAKDPNPN NPA

UniProtKB: Major capsid protein

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Macromolecule #2: Virion associated protein

MacromoleculeName: Virion associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 15.819934 KDa
SequenceString:
MALIQSDFAQ GIRMTPVPDC AGDVTACRFD ITLKNAPAAG DIIELGVLPG NAVPVEAILD VDDLDTGGAP TITLDVGIMS GPVGKNDPA RTCGNELFAA STVGQAGGVV RATASSAFRI QKAEDHRSVG VKVAAGPATG AAGKTIALIL FYVQGTSQ

UniProtKB: Virion associated 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

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40792
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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