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- PDB-1bvp: THE CRYSTAL STRUCTURE OF BLUETONGUE VIRUS VP7 -

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Basic information

Entry
Database: PDB / ID: 1bvp
TitleTHE CRYSTAL STRUCTURE OF BLUETONGUE VIRUS VP7
ComponentsBLUETONGUE VIRUS COAT PROTEIN VP7
KeywordsVIRAL PROTEIN / VIRUS / VP7 / TRIMER
Function / homology
Function and homology information


viral outer capsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity
Similarity search - Function
Bluetongue Virus 10, subunit 1; domain 3 / Bluetongue Virus 10, subunit 1, domain 3 / Bluetongue Virus 10, subunit 1; domain 1 / Bluetongue Virus 10, subunit 1, domain 1 / Orbivirus inner capsid protein VP7 / Orbivirus inner capsid protein VP7, N-terminal / Orbivirus inner capsid protein VP7, C-terminal / Orbivirus inner capsid protein VP7 / Jelly Rolls - #170 / Virus capsid protein, alpha-helical ...Bluetongue Virus 10, subunit 1; domain 3 / Bluetongue Virus 10, subunit 1, domain 3 / Bluetongue Virus 10, subunit 1; domain 1 / Bluetongue Virus 10, subunit 1, domain 1 / Orbivirus inner capsid protein VP7 / Orbivirus inner capsid protein VP7, N-terminal / Orbivirus inner capsid protein VP7, C-terminal / Orbivirus inner capsid protein VP7 / Jelly Rolls - #170 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBluetongue virus
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsStuart, D. / Grimes, J.
Citation
Journal: Nature / Year: 1995
Title: The crystal structure of bluetongue virus VP7.
Authors: Grimes, J. / Basak, A.K. / Roy, P. / Stuart, D.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Preliminary Crystallographic Study Bluetongue Virus Capsid Protein, Vp7
Authors: Basak, A.K. / Stuart, D. / Roy, P.
History
DepositionFeb 17, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: BLUETONGUE VIRUS COAT PROTEIN VP7
2: BLUETONGUE VIRUS COAT PROTEIN VP7
3: BLUETONGUE VIRUS COAT PROTEIN VP7
4: BLUETONGUE VIRUS COAT PROTEIN VP7
5: BLUETONGUE VIRUS COAT PROTEIN VP7
6: BLUETONGUE VIRUS COAT PROTEIN VP7


Theoretical massNumber of molelcules
Total (without water)231,4706
Polymers231,4706
Non-polymers00
Water00
1
1: BLUETONGUE VIRUS COAT PROTEIN VP7
2: BLUETONGUE VIRUS COAT PROTEIN VP7
3: BLUETONGUE VIRUS COAT PROTEIN VP7


Theoretical massNumber of molelcules
Total (without water)115,7353
Polymers115,7353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-56 kcal/mol
Surface area36620 Å2
MethodPISA
2
4: BLUETONGUE VIRUS COAT PROTEIN VP7
5: BLUETONGUE VIRUS COAT PROTEIN VP7
6: BLUETONGUE VIRUS COAT PROTEIN VP7


Theoretical massNumber of molelcules
Total (without water)115,7353
Polymers115,7353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15590 Å2
ΔGint-56 kcal/mol
Surface area36630 Å2
MethodPISA
3
1: BLUETONGUE VIRUS COAT PROTEIN VP7
2: BLUETONGUE VIRUS COAT PROTEIN VP7
3: BLUETONGUE VIRUS COAT PROTEIN VP7

4: BLUETONGUE VIRUS COAT PROTEIN VP7
5: BLUETONGUE VIRUS COAT PROTEIN VP7
6: BLUETONGUE VIRUS COAT PROTEIN VP7


Theoretical massNumber of molelcules
Total (without water)231,4706
Polymers231,4706
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area34790 Å2
ΔGint-140 kcal/mol
Surface area69660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.600, 110.200, 129.800
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 1 338 / 2: CIS PROLINE - PRO 2 338 / 3: CIS PROLINE - PRO 3 338 / 4: CIS PROLINE - PRO 4 338 / 5: CIS PROLINE - PRO 5 338 / 6: CIS PROLINE - PRO 6 338
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.14543, 0.67629, -0.72214), (-0.63411, -0.49656, -0.59274), (-0.75945, 0.54411, 0.35662)13.75691, 121.46453, 15.26016
2given(0.14324, -0.63096, -0.76247), (0.67663, -0.49981, 0.54071), (-0.72226, -0.59336, 0.35534)86.88766, 43.31865, 76.52478
3given(-0.99998, 0.00266, -0.00651), (0.00204, 0.99556, 0.09409), (0.00673, 0.09407, -0.99554)-40.40277, -14.51652, 185.40674
4given(-0.14325, -0.67863, 0.72038), (-0.7013, -0.44399, -0.55772), (0.69832, -0.5851, -0.41232)-54.40217, 107.98046, 181.39107
5given(-0.13779, 0.63372, 0.76119), (0.60571, -0.55415, 0.57099), (0.78367, 0.53974, -0.30749)-127.61971, 35.81133, 113.78906
DetailsVP7 FORMS A TRIMER IN CRYSTAL, SOLUTION, AND IN THE VIRUS. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 1 1 .. N 349 2 1 .. N 349 0.0005 M2 1 1 .. N 349 3 1 .. N 349 0.0005 M3 1 1 .. N 349 4 1 .. N 349 0.0005 M4 1 1 .. N 349 5 1 .. N 349 0.0005 M5 1 1 .. N 349 6 1 .. N 349 0.0005

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Components

#1: Protein
BLUETONGUE VIRUS COAT PROTEIN VP7


Mass: 38578.348 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bluetongue virus / Genus: Orbivirus / Strain: (serotype 10 / American isolate) / References: UniProt: P69361

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
210 %(w/v)PEG35001reservoir
30.1 Msodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 54361 / % possible obs: 81 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.105
Reflection
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.105

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.6→15 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 54361
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16218 0 0 0 16218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.85

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