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- PDB-9eqp: N-terminal domain of Infectious Bursal Disease Virus (IBDV) VP3 -

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Basic information

Entry
Database: PDB / ID: 9eqp
TitleN-terminal domain of Infectious Bursal Disease Virus (IBDV) VP3
ComponentsCapsid protein VP3
KeywordsVIRAL PROTEIN / dsRNA binding protein / Birnavirus / IBDV
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFerrero, D.S. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117976GB-I00 Spain
CitationJournal: Pnas Nexus / Year: 2024
Title: Structure of the aminoterminal domain of the birnaviral multifunctional VP3 protein and its unexplored critical role.
Authors: Ferrero, D.S. / Gimenez, M.C. / Sagar, A. / Rodriguez, J.M. / Caston, J.R. / Terebiznik, M.R. / Bernado, P. / Verdaguer, N.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP3
B: Capsid protein VP3
C: Capsid protein VP3
D: Capsid protein VP3
E: Capsid protein VP3
F: Capsid protein VP3
G: Capsid protein VP3
I: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)120,1428
Polymers120,1428
Non-polymers00
Water00
1
A: Capsid protein VP3
B: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)30,0362
Polymers30,0362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-16 kcal/mol
Surface area14220 Å2
MethodPISA
2
C: Capsid protein VP3
E: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)30,0362
Polymers30,0362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-10 kcal/mol
Surface area14610 Å2
MethodPISA
3
D: Capsid protein VP3
F: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)30,0362
Polymers30,0362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-9 kcal/mol
Surface area14360 Å2
MethodPISA
4
G: Capsid protein VP3
I: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)30,0362
Polymers30,0362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-13 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.687, 111.416, 277.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Capsid protein VP3


Mass: 15017.759 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Plasmid: pRSET-C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61825
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.8 M LiSO4, 0.05 M Sodium Cacodylate pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.5→47.6 Å / Num. obs: 19960 / % possible obs: 97.6 % / Redundancy: 4.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1868 / Rpim(I) all: 0.0907 / Rrim(I) all: 0.209 / Net I/σ(I): 8.17
Reflection shellResolution: 3.5→3.68 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.237 / Num. unique obs: 4736 / CC1/2: 0.529 / Rpim(I) all: 0.5955 / Rrim(I) all: 1.382 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→47.6 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 985 4.94 %Random selection
Rwork0.2381 ---
obs0.2392 19924 96.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8353 0 0 0 8353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.859
X-RAY DIFFRACTIONf_dihedral_angle_d15.3733323
X-RAY DIFFRACTIONf_chiral_restr0.0531184
X-RAY DIFFRACTIONf_plane_restr0.0221558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.680.33981380.3472693X-RAY DIFFRACTION98
3.68-3.920.34431350.29642668X-RAY DIFFRACTION97
3.92-4.220.27911330.27022696X-RAY DIFFRACTION97
4.22-4.640.27981080.2192722X-RAY DIFFRACTION97
4.64-5.310.23871400.22872677X-RAY DIFFRACTION96
5.31-6.690.26691570.25822697X-RAY DIFFRACTION96
6.69-47.60.2161740.18612786X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0213-2.2781-1.25863.08260.7762.3959-0.0442-0.19990.3143-0.07310.1207-0.3433-0.0750.2786-0.02030.6215-0.0226-0.00520.77180.02150.736423.676-1.1088-44.7324
24.8862-1.26430.37933.14580.15442.31890.12190.0817-0.1549-0.3145-0.15980.5156-0.28-0.0387-0.00230.69260.0476-0.0180.76880.08080.72223.8506-1.2301-42.6344
33.7862-1.55882.66193.3591-1.93845.1769-0.1207-0.1732-0.1765-0.11190.0348-0.03720.121-0.0957-0.0450.77690.00430.04110.7729-0.0430.772327.3486-20.008-60.2387
42.1487-0.4614-1.46171.93670.93884.2016-0.3188-0.1238-0.0264-0.31070.15980.44470.4089-0.19750.05871.12350.0624-0.17350.83490.06590.9453-2.290617.0195-57.4663
53.3806-0.70341.87312.2138-1.40885.95870.15330.5899-0.046-0.7003-0.01660.2580.36660.4832-0.07171.0391-0.0995-0.10740.8467-0.10250.945117.6511-20.7798-77.4076
60.2352-0.854-0.7682.31221.77855.57350.05450.12940.0826-0.38160.0284-0.2498-0.1693-0.1130.04021.2221-0.09-0.10290.9042-0.00870.9447.166117.8999-75.1955
71.73091.6165-1.33832.24-2.12234.54440.1389-0.18560.15210.27120.18660.4277-0.0668-0.687-0.08830.8940.16750.14621.26310.23230.77385.6084-21.907-9.404
80.55460.235-0.65871.195-0.92333.1189-0.14920.3294-0.4444-0.35760.20170.16061.0829-0.8879-0.07180.9864-0.06010.10791.28650.26650.8887-3.4014-39.6694-7.8346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 91 through 220)
2X-RAY DIFFRACTION2(chain 'B' and resid 91 through 221)
3X-RAY DIFFRACTION3(chain 'C' and resid 91 through 220)
4X-RAY DIFFRACTION4(chain 'D' and resid 91 through 219)
5X-RAY DIFFRACTION5(chain 'E' and resid 91 through 220)
6X-RAY DIFFRACTION6(chain 'F' and resid 91 through 220)
7X-RAY DIFFRACTION7(chain 'G' and resid 91 through 220)
8X-RAY DIFFRACTION8(chain 'I' and resid 91 through 220)

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