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- PDB-8h89: Capsid of Ralstonia phage GP4 -

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Basic information

Entry
Database: PDB / ID: 8h89
TitleCapsid of Ralstonia phage GP4
Components
  • Major capsid protein
  • Virion associated protein
KeywordsVIRUS / Ralstonia phage GP4 / Complex
Function / homologyProtein of unknown function DUF4043 / Protein of unknown function (DUF4043) / Virion associated protein / Major capsid protein
Function and homology information
Biological speciesRalstonia phage GP4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLiu, H.R. / Chen, W.Y.
Funding support China, 4items
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, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 14, 2022Group: Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3]
Revision 1.3Apr 19, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.4Aug 30, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Virion associated protein
K: Virion associated protein
L: Virion associated protein
M: Virion associated protein
N: Virion associated protein
O: Virion associated protein
P: Virion associated protein
Q: Virion associated protein
R: Virion associated protein


Theoretical massNumber of molelcules
Total (without water)509,75518
Polymers509,75518
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Virion associated protein
K: Virion associated protein
L: Virion associated protein
M: Virion associated protein
N: Virion associated protein
O: Virion associated protein
P: Virion associated protein
Q: Virion associated protein
R: Virion associated protein
x 60


Theoretical massNumber of molelcules
Total (without water)30,585,3221080
Polymers30,585,3221080
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Virion associated protein
K: Virion associated protein
L: Virion associated protein
M: Virion associated protein
N: Virion associated protein
O: Virion associated protein
P: Virion associated protein
Q: Virion associated protein
R: Virion associated protein
x 5


  • icosahedral pentamer
  • 2.55 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,548,77790
Polymers2,548,77790
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Virion associated protein
K: Virion associated protein
L: Virion associated protein
M: Virion associated protein
N: Virion associated protein
O: Virion associated protein
P: Virion associated protein
Q: Virion associated protein
R: Virion associated protein
x 6


  • icosahedral 23 hexamer
  • 3.06 MDa, 108 polymers
Theoretical massNumber of molelcules
Total (without water)3,058,532108
Polymers3,058,532108
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein
Major capsid protein / gp2


Mass: 40819.551 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GTT3
#2: Protein
Virion associated protein / gp1


Mass: 15819.934 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GTT2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ralstonia phage GP4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Ralstonia phage GP4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3800 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40792 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00536163
ELECTRON MICROSCOPYf_angle_d0.64648951
ELECTRON MICROSCOPYf_dihedral_angle_d5.3175105
ELECTRON MICROSCOPYf_chiral_restr0.0485429
ELECTRON MICROSCOPYf_plane_restr0.0056533

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