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- PDB-2btv: ATOMIC MODEL FOR BLUETONGUE VIRUS (BTV) CORE -

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Basic information

Entry
Database: PDB / ID: 2btv
TitleATOMIC MODEL FOR BLUETONGUE VIRUS (BTV) CORE
Components
  • PROTEIN (VP3 CORE PROTEIN)
  • PROTEIN (VP7 CORE PROTEIN)
KeywordsVIRUS / VIRUS/VIRAL PROTEIN / Icosahedral virus
Function / homology
Function and homology information


viral outer capsid / virion component => GO:0044423 / 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 / Inner layer core protein VP3, Orbivirus / Orbivirus VP3 (T2) protein ...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 / Inner layer core protein VP3, Orbivirus / Orbivirus VP3 (T2) protein / Inner layer core protein VP3, Reovirus / 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
Core protein VP7 / Core protein VP3
Similarity search - Component
Biological speciesBluetongue virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGrimes, J.M. / Burroughs, J.N. / Gouet, P. / Diprose, J.M. / Malby, R. / Zientras, S. / Mertens, P.P.C. / Stuart, D.I.
CitationJournal: Nature / Year: 1998
Title: The atomic structure of the bluetongue virus core.
Authors: Grimes, J.M. / Burroughs, J.N. / Gouet, P. / Diprose, J.M. / Malby, R. / Zientara, S. / Mertens, P.P. / Stuart, D.I.
History
DepositionSep 5, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (VP3 CORE PROTEIN)
B: PROTEIN (VP3 CORE PROTEIN)
P: PROTEIN (VP7 CORE PROTEIN)
C: PROTEIN (VP7 CORE PROTEIN)
D: PROTEIN (VP7 CORE PROTEIN)
Q: PROTEIN (VP7 CORE PROTEIN)
E: PROTEIN (VP7 CORE PROTEIN)
F: PROTEIN (VP7 CORE PROTEIN)
R: PROTEIN (VP7 CORE PROTEIN)
G: PROTEIN (VP7 CORE PROTEIN)
H: PROTEIN (VP7 CORE PROTEIN)
S: PROTEIN (VP7 CORE PROTEIN)
I: PROTEIN (VP7 CORE PROTEIN)
J: PROTEIN (VP7 CORE PROTEIN)
T: PROTEIN (VP7 CORE PROTEIN)


Theoretical massNumber of molelcules
Total (without water)707,82415
Polymers707,82415
Non-polymers00
Water0
1
A: PROTEIN (VP3 CORE PROTEIN)
B: PROTEIN (VP3 CORE PROTEIN)
P: PROTEIN (VP7 CORE PROTEIN)
C: PROTEIN (VP7 CORE PROTEIN)
D: PROTEIN (VP7 CORE PROTEIN)
Q: PROTEIN (VP7 CORE PROTEIN)
E: PROTEIN (VP7 CORE PROTEIN)
F: PROTEIN (VP7 CORE PROTEIN)
R: PROTEIN (VP7 CORE PROTEIN)
G: PROTEIN (VP7 CORE PROTEIN)
H: PROTEIN (VP7 CORE PROTEIN)
S: PROTEIN (VP7 CORE PROTEIN)
I: PROTEIN (VP7 CORE PROTEIN)
J: PROTEIN (VP7 CORE PROTEIN)
T: PROTEIN (VP7 CORE PROTEIN)
x 60


Theoretical massNumber of molelcules
Total (without water)42,469,424900
Polymers42,469,424900
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: PROTEIN (VP3 CORE PROTEIN)
B: PROTEIN (VP3 CORE PROTEIN)
P: PROTEIN (VP7 CORE PROTEIN)
C: PROTEIN (VP7 CORE PROTEIN)
D: PROTEIN (VP7 CORE PROTEIN)
Q: PROTEIN (VP7 CORE PROTEIN)
E: PROTEIN (VP7 CORE PROTEIN)
F: PROTEIN (VP7 CORE PROTEIN)
R: PROTEIN (VP7 CORE PROTEIN)
G: PROTEIN (VP7 CORE PROTEIN)
H: PROTEIN (VP7 CORE PROTEIN)
S: PROTEIN (VP7 CORE PROTEIN)
I: PROTEIN (VP7 CORE PROTEIN)
J: PROTEIN (VP7 CORE PROTEIN)
T: PROTEIN (VP7 CORE PROTEIN)
x 5


  • icosahedral pentamer
  • 3.54 MDa, 75 polymers
Theoretical massNumber of molelcules
Total (without water)3,539,11975
Polymers3,539,11975
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: PROTEIN (VP3 CORE PROTEIN)
B: PROTEIN (VP3 CORE PROTEIN)
P: PROTEIN (VP7 CORE PROTEIN)
C: PROTEIN (VP7 CORE PROTEIN)
D: PROTEIN (VP7 CORE PROTEIN)
Q: PROTEIN (VP7 CORE PROTEIN)
E: PROTEIN (VP7 CORE PROTEIN)
F: PROTEIN (VP7 CORE PROTEIN)
R: PROTEIN (VP7 CORE PROTEIN)
G: PROTEIN (VP7 CORE PROTEIN)
H: PROTEIN (VP7 CORE PROTEIN)
S: PROTEIN (VP7 CORE PROTEIN)
I: PROTEIN (VP7 CORE PROTEIN)
J: PROTEIN (VP7 CORE PROTEIN)
T: PROTEIN (VP7 CORE PROTEIN)
x 6


  • icosahedral 23 hexamer
  • 4.25 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)4,246,94290
Polymers4,246,94290
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
6
A: PROTEIN (VP3 CORE PROTEIN)
B: PROTEIN (VP3 CORE PROTEIN)
P: PROTEIN (VP7 CORE PROTEIN)
C: PROTEIN (VP7 CORE PROTEIN)
D: PROTEIN (VP7 CORE PROTEIN)
Q: PROTEIN (VP7 CORE PROTEIN)
E: PROTEIN (VP7 CORE PROTEIN)
F: PROTEIN (VP7 CORE PROTEIN)
R: PROTEIN (VP7 CORE PROTEIN)
G: PROTEIN (VP7 CORE PROTEIN)
H: PROTEIN (VP7 CORE PROTEIN)
S: PROTEIN (VP7 CORE PROTEIN)
I: PROTEIN (VP7 CORE PROTEIN)
J: PROTEIN (VP7 CORE PROTEIN)
T: PROTEIN (VP7 CORE PROTEIN)
x 30


  • crystal asymmetric unit, crystal frame
  • 21.2 MDa, 450 polymers
Theoretical massNumber of molelcules
Total (without water)21,234,712450
Polymers21,234,712450
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)795.600, 821.800, 753.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.80831985, -0.51865711, 0.27859258), (0.48134289, 0.30971414, -0.81999157), (0.3390104, 0.79691402, 0.5)-52.57042, 154.73241, 94.35
3generate(0.49817484, -0.35786195, 0.78978266), (0.26017204, -0.80719184, -0.52986021), (0.82712293, 0.46944239, -0.30901699)-149.03198, 99.98462, 247.0115
4generate(0.49817484, 0.26017204, 0.82712293), (-0.35786195, -0.80719184, 0.46944239), (0.78978266, -0.52986021, -0.30901699)-156.07809, -88.58378, 247.0115
5generate(0.80831985, 0.48134289, 0.3390104), (-0.51865711, 0.30971414, 0.79691402), (0.27859258, -0.81999157, 0.5)-63.97126, -150.37767, 94.35
6generate(0.99721141, -0.07462845), (-0.07462845, -0.99721141), (-1)377.39999
7generate(0.7701439, -0.54032428, 0.3390104), (-0.54032428, -0.2701439, 0.79691402), (-0.3390104, -0.79691402, -0.5)-63.97126, -150.37767, 283.04999
8generate(0.4773694, -0.29662454, 0.82712293), (-0.29662454, 0.83164759, 0.46944239), (-0.82712293, -0.46944239, 0.30901699)-156.07809, -88.58378, 130.38849
9generate(0.52349232, 0.319686, 0.78978266), (0.319686, 0.78552467, -0.52986021), (-0.78978266, 0.52986021, 0.30901699)-149.03198, 99.98462, 130.38849
10generate(0.84477235, 0.45688713, 0.27859258), (0.45688713, -0.34477235, -0.81999157), (-0.27859258, 0.81999157, -0.5)-52.57042, 154.73241, 283.04999
11generate(0.03731423, -0.0013943, 0.99930261), (0.9986057, -0.03731423, -0.03734027), (0.03734027, 0.99930261)-188.5684, 7.04611, 188.7
12generate(0.36826467, 0.77657313, 0.51119008), (0.77657313, -0.55924768, 0.29013136), (0.51119008, 0.29013136, -0.80901699)-96.46157, -54.74779, 341.3615
13generate(0.84477235, 0.45688713, -0.27859258), (0.45688713, -0.34477235, 0.81999157), (0.27859258, -0.81999157, -0.5)52.57042, -154.73241, 283.04999
14generate(0.80831985, -0.51865711, -0.27859258), (0.48134289, 0.30971414, 0.81999157), (-0.3390104, -0.79691402, 0.5)52.57042, -154.73241, 94.35
15generate(0.30928328, -0.80189061, 0.51119008), (0.81614338, 0.49973371, 0.29013136), (-0.48811253, 0.32747162, 0.80901699)-96.46157, -54.74779, 36.03849
16generate(0.03731423, -0.0013943, -0.99930261), (0.9986057, -0.03731423, 0.03734027), (-0.03734027, -0.99930261)188.5684, -7.04611, 188.7
17generate(-0.30928328, -0.81614338, -0.48811253), (0.80189061, -0.49973371, 0.32747162), (-0.51119008, -0.29013136, 0.80901699)92.10683, -61.79389, 36.03849
18generate(-0.80831985, -0.48134289, 0.3390104), (0.51865711, -0.30971414, 0.79691402), (-0.27859258, 0.81999157, 0.5)-63.97126, -150.37767, 94.35
19generate(-0.7701439, 0.54032428, 0.3390104), (0.54032428, 0.2701439, 0.79691402), (0.3390104, 0.79691402, -0.5)-63.97126, -150.37767, 283.04999
20generate(-0.2475133, 0.83694882, -0.48811253), (0.83694882, 0.43849631, 0.32747162), (0.48811253, -0.32747162, -0.80901699)92.10683, -61.79389, 341.3615
21generate(0.03731423, 0.9986057, 0.03734027), (-0.0013943, -0.03731423, 0.99930261), (0.99930261, -0.03734027)-7.04611, -188.5684, 188.7
22generate(0.52349232, 0.319686, -0.78978266), (0.319686, 0.78552467, 0.52986021), (0.78978266, -0.52986021, 0.30901699)149.03198, -99.98462, 130.38849
23generate(0.30928328, -0.80189061, -0.51119008), (0.81614338, 0.49973371, -0.29013136), (0.48811253, -0.32747162, 0.80901699)96.46157, 54.74779, 36.03849
24generate(-0.30928328, -0.81614338, 0.48811253), (0.80189061, -0.49973371, -0.32747162), (0.51119008, 0.29013136, 0.80901699)-92.10683, 61.79389, 36.03849
25generate(-0.4773694, 0.29662454, 0.82712293), (0.29662454, -0.83164759, 0.46944239), (0.82712293, 0.46944239, 0.30901699)-156.07809, -88.58378, 130.38849
26generate(-0.03731423, -0.9986057, 0.03734027), (0.0013943, 0.03731423, 0.99930261), (-0.99930261, 0.03734027)-7.04611, -188.5684, 188.7
27generate(-0.49817484, -0.26017204, 0.82712293), (0.35786195, 0.80719184, 0.46944239), (-0.78978266, 0.52986021, -0.30901699)-156.07809, -88.58378, 247.0115
28generate(-0.2475133, 0.83694882, 0.48811253), (0.83694882, 0.43849631, -0.32747162), (-0.48811253, 0.32747162, -0.80901699)-92.10683, 61.79389, 341.3615
29generate(0.36826467, 0.77657313, -0.51119008), (0.77657313, -0.55924768, -0.29013136), (-0.51119008, -0.29013136, -0.80901699)96.46157, 54.74779, 341.3615
30generate(0.49817484, -0.35786195, -0.78978266), (0.26017204, -0.80719184, 0.52986021), (-0.82712293, -0.46944239, -0.30901699)149.03198, -99.98462, 247.0115

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Components

#1: Protein PROTEIN (VP3 CORE PROTEIN) / T2A / T2B


Mass: 103367.406 Da / Num. of mol.: 2 / Fragment: INNER LAYER CORE PROTEIN / Source method: isolated from a natural source
Source: (natural) Bluetongue virus (serotype 1 / isolate South Africa)
Genus: Orbivirus / Species: Bluetongue virusBluetongue disease / Strain: STEROTYPE 1 (SOUTH AFRICA) / References: UniProt: P56582
#2: Protein
PROTEIN (VP7 CORE PROTEIN) / T13


Mass: 38545.301 Da / Num. of mol.: 13 / Fragment: OUTER LAYER CORE PROTEIN / Source method: isolated from a natural source
Source: (natural) Bluetongue virus (serotype 1 / isolate South Africa)
Genus: Orbivirus / Species: Bluetongue virusBluetongue disease / Strain: STEROTYPE 1 (SOUTH AFRICA) / References: UniProt: P18259
Compound detailsCAPSID STRUCTURE OF THE CORE PARTICLE OF BTV. THIS LARGE MACROMOLECULAR ASSEMBLY CONTAINS ...CAPSID STRUCTURE OF THE CORE PARTICLE OF BTV. THIS LARGE MACROMOLECULAR ASSEMBLY CONTAINS APPROXIMATELY 1000 POLYPEPTIDE CHAINS. THIS CORE PARTICLE HAS A A DOUBLE SHELL ARCHITECTURE, WITH 780 COPIES OF VP7 CLOAKING AN INNER LAYER OF 120 COPIES OF VP3. THIS CAPSID ENCASES THE DSRNA GENOME WHICH HAS TRANSCRIPTASE, HELICASE AND GUANYLYLTRANSFERASE ACTIVITY ASSOCIATED WITH IT. THE MODEL CONTAINS 15 PROTEINS, 13 COPIES OF VP7 AND 2 COPIES OF VP3. THIS REPRESENTS THE VIRAL ASYMMETRIC UNIT. THE 13 COPIES OF VP7 ARE ARRANGED AS 4 AND 1/3 TRIMERS IN THE VIRAL ASYMMETRIC UNIT, REFERENCED AS TRIMERS VP7P VP7Q VP7R VP7S AND VP7T. VP3A IS THE FIRST MOLECULE OF VP3 (AS REFERENCED IN THE PAPER). IT IS IN ONE PIECE WITH SEGID 2011 AND RUNS FROM RESIDUE 57-901 IN THE ELECTRON DENSITY MAP. VP3B IS THE SECOND MOLECULE. IT IS IN 2 SEPERATE PIECES WITH SEGIDS 1011 AND 1021. IT RUNS FROM 7-803 AND 814-901 EACH TRIMER OF VP7 (EXCEPT T WHICH SITS ON THE ICOSAHEDRAL 3-FOLD AXIS) IS SPLIT INTO 3 MONOMERS VP7P MOLECULE 1 HAS SEGID 1101, VP7P MOLECULE 2 HAS SEGID 1201, VP7P MOLECULE 3 HAS SEGID 1301, VP7Q MOLECULE 1 HAS SEGID 2101, VP7Q MOLECULE 2 HAS SEGID 2201, VP7Q MOLECULE 3 HAS SEGID 2301, VP7R MOLECULE 1 HAS SEGID 3101, VP7R MOLECULE 2 HAS SEGID 3201, VP7R MOLECULE 3 HAS SEGID 3301, VP7S MOLECULE 1 HAS SEGID 4101, VP7S MOLECULE 2 HAS SEGID 4201, VP7S MOLECULE 3 HAS SEGID 4301, VP7T MOLECULE 1 HAS SEGID 5101. (THE TRIMER IS GENERATED BY THE ICOSAHEDRAL SYMMETRY)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1000

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Sample preparation

CrystalDescription: OVER 1000 CRYSTALS EXAMINED. DATA WERE COLLECTED DRUNIG 1995-1997. WAVELENGTHES BETWEEN 0.87 - 1.00.
Crystal growpH: 8
Details: 15% AMMONIUM SULPHATE 25% ETHYLENE GLYCOL 0.1M TRIS/HCL BUFFER PH8.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Burroughs, J.N., (1995) Virology, 210, 217.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111-16 %satammonium sulfate1reservoir
20.1 MTris-HCl1reservoir
315 %ethylene glycol1reservoir
43 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 3299866 / % possible obs: 54 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.229 / Net I/σ(I): 2.9
Reflection shellResolution: 3.5→4 Å / Redundancy: 1.06 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 0.72 / % possible all: 7.8
Reflection
*PLUS
Num. obs: 21510811 / % possible obs: 53.5 % / Num. measured all: 3299866
Reflection shell
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.677

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→100 Å / Isotropic thermal model: INDIVIDUAL ATOM RESTRAINT / σ(F): 0
Details: BOND (A**2): 5.0 ANGLE (A**2): 8.3 METHOD USED: ADDITION OF BULK SOLVENT IN X-PLOR KSOL: 0.30 BSOL: 60.0
RfactorNum. reflection% reflection
Rwork0.266 --
obs0.266 3291956 54 %
Refinement stepCycle: LAST / Resolution: 3.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49062 0 0 0 49062
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.406
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.43
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
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
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 100 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.43
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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