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- PDB-7vrp: Structure of infectious bursal disease virus Gx strain -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7vrp
TitleStructure of infectious bursal disease virus Gx strain
ComponentsStructural polyprotein
KeywordsVIRUS / IBDV / icosahedral / very virulent
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. ...icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesAvian infectious bursal disease virus (Gumboro virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBao, K.Y. / Zhu, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31430087 China
National Natural Science Foundation of China (NSFC)31425007 China
CitationJournal: Sci Bull (Beijing) / Year: 2022
Title: Cryo-EM structures of infectious bursal disease viruses with different virulences provide insights into their assembly and invasion
Authors: Bao, K. / Qi, X. / Lia, Y. / Gong, M. / Wang, M. / Zhu, P.
History
DepositionOct 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural polyprotein
L: Structural polyprotein
M: Structural polyprotein
K: Structural polyprotein
I: Structural polyprotein
F: Structural polyprotein
E: Structural polyprotein
C: Structural polyprotein
H: Structural polyprotein
J: Structural polyprotein
D: Structural polyprotein
G: Structural polyprotein
B: Structural polyprotein


Theoretical massNumber of molelcules
Total (without water)611,37513
Polymers611,37513
Non-polymers00
Water00
1
A: Structural polyprotein
L: Structural polyprotein
M: Structural polyprotein
K: Structural polyprotein
I: Structural polyprotein
F: Structural polyprotein
E: Structural polyprotein
C: Structural polyprotein
H: Structural polyprotein
J: Structural polyprotein
D: Structural polyprotein
G: Structural polyprotein
B: Structural polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)36,682,519780
Polymers36,682,519780
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: Structural polyprotein
L: Structural polyprotein
M: Structural polyprotein
K: Structural polyprotein
I: Structural polyprotein
F: Structural polyprotein
E: Structural polyprotein
C: Structural polyprotein
H: Structural polyprotein
J: Structural polyprotein
D: Structural polyprotein
G: Structural polyprotein
B: Structural polyprotein
x 5


  • icosahedral pentamer
  • 3.06 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)3,056,87765
Polymers3,056,87765
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Structural polyprotein
L: Structural polyprotein
M: Structural polyprotein
K: Structural polyprotein
I: Structural polyprotein
F: Structural polyprotein
E: Structural polyprotein
C: Structural polyprotein
H: Structural polyprotein
J: Structural polyprotein
D: Structural polyprotein
G: Structural polyprotein
B: Structural polyprotein
x 6


  • icosahedral 23 hexamer
  • 3.67 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)3,668,25278
Polymers3,668,25278
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Structural polyprotein / Structural protein VP2 / PP


Mass: 47028.871 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Avian infectious bursal disease virus (Gumboro virus)
References: UniProt: Q6SZ77, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: Infectious bursal disease virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Infectious bursal disease virus (Gumboro virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Gallus gallus
Buffer solutionpH: 7.2
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 47.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3524 / Symmetry type: POINT

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