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- PDB-1ahs: CRYSTAL STRUCTURE OF THE TOP DOMAIN OF AFRICAN HORSE SICKNESS VIR... -

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Basic information

Entry
Database: PDB / ID: 1ahs
TitleCRYSTAL STRUCTURE OF THE TOP DOMAIN OF AFRICAN HORSE SICKNESS VIRUS VP7
ComponentsAFRICAN HORSE SICKNESS VIRUS (SEROTYPE 4) VP7
KeywordsVIRAL PROTEIN / CORE PROTEIN / GLYCOPROTEIN / COAT PROTEIN (VIRAL)
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
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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesAfrican horsesickness virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR/molecular replacement / Resolution: 2.3 Å
AuthorsStuart, D. / Gouet, P.
Citation
Journal: J.Virol. / Year: 1996
Title: Crystal structure of the top domain of African horse sickness virus VP7: comparisons with bluetongue virus VP7.
Authors: Basak, A.K. / Gouet, P. / Grimes, J. / Roy, P. / Stuart, D.
#1: Journal: Nature / Year: 1995
Title: The Crystal Structure of Bluetongue Virus Vp7
Authors: Grimes, J. / Basak, A.K. / Roy, P. / Stuart, D.
History
DepositionMar 18, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: 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: AFRICAN HORSE SICKNESS VIRUS (SEROTYPE 4) VP7
B: AFRICAN HORSE SICKNESS VIRUS (SEROTYPE 4) VP7
C: AFRICAN HORSE SICKNESS VIRUS (SEROTYPE 4) VP7


Theoretical massNumber of molelcules
Total (without water)40,3293
Polymers40,3293
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-8 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.200, 157.200, 57.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2202, -0.3937, 0.8925), (0.7919, -0.4621, -0.3992), (0.5696, 0.7947, 0.21)24.6377, -0.7881, -24.5936
2given(0.2462, 0.7918, 0.559), (-0.4141, -0.4355, 0.7993), (0.8763, -0.4282, 0.2207)7.9918, 29.195, -15.8854

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Components

#1: Protein AFRICAN HORSE SICKNESS VIRUS (SEROTYPE 4) VP7


Mass: 13443.129 Da / Num. of mol.: 3 / Fragment: TOP DOMAIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) African horsesickness virus / Genus: Orbivirus / References: UniProt: P36325
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE TRIMERIC FRAGMENT OF AFRICAN HORSESICKNESS VIRUS CAN BE SUPERIMPOSED WITH THE 'TOP DOMAIN' OF ...THE TRIMERIC FRAGMENT OF AFRICAN HORSESICKNESS VIRUS CAN BE SUPERIMPOSED WITH THE 'TOP DOMAIN' OF BLUETONGUE VIRUS VP7 WITH AN RMS DEVIATION (CA ATOMS) OF 1.2 ANGSTROMS. THE WHOLE SEQUENCES OF THESE TWO PROTEINS HAVE AN IDENTITY OF 43% AND THE DEPOSITORS ASSUME THAT THE MISSING DOMAIN OF AFRICAN HORSESICKNESS HAS A CA TRACE SIMILAR TO THE ONE OF BLUETONGUE VIRUS VP7.

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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: 4.42 Å3/Da / Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMTris-HCl1drop
22.8 Murea1drop
36-8 mg/mlprotein1drop
445-48 %satammonium sulfate1reservoir
510 mMTris-HCl1reservoir

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength
ROTATING ANODE11.5418
SYNCHROTRONPhoton Factory BL-6A20.98
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJun 15, 1993
WEISSENBERG2DIFFRACTOMETERJun 15, 1993
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
ReflectionResolution: 2.3→30 Å / Num. obs: 29456 / % possible obs: 91 % / Observed criterion σ(I): -2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR/molecular replacement
Starting model: 1BVP

1bvp


Resolution: 2.3→15 Å / σ(F): 0
Details: THE REFINEMENT WAS CARRIED OUT AGAINST A MERGE OF THE IN-HOUSE AND SYNCHROTRON DATA. THE THREE SUBUNITS WERE REFINED INDEPENDENTLY. THE WATER MOLECULE HOH 1 LOCATED ALONG THE PSEUDO ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST A MERGE OF THE IN-HOUSE AND SYNCHROTRON DATA. THE THREE SUBUNITS WERE REFINED INDEPENDENTLY. THE WATER MOLECULE HOH 1 LOCATED ALONG THE PSEUDO MOLECULAR THREE-FOLD AXIS HAS AN UNLIKELY LOW TEMPERATURE FACTOR OF 2.00 A**2 AND MAY BE A CHLORIDE ION. THE WATER MOLECULE HOH 1 LOCATED ALONG THE PSEUDO MOLECULAR THREE-FOLD AXIS HAS AN UNLIKELY LOW TEMPERATURE FACTOR OF 2.00 A**2 AND MAY BE A CHLORIDE ION.
RfactorNum. reflection% reflection
Rwork0.213 --
obs0.213 28590 91 %
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 0 61 2728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.3
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

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