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- PDB-1qhd: CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROT... -

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Basic information

Entry
Database: PDB / ID: 1qhd
TitleCRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS
ComponentsVIRAL CAPSID VP6
KeywordsVIRAL PROTEIN / VIRAL CAPSID PROTEIN
Function / homology
Function and homology information


viral intermediate capsid / T=13 icosahedral viral capsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / metal ion binding
Similarity search - Function
Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle ...Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Intermediate capsid protein VP6
Similarity search - Component
Biological speciesBovine rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.95 Å
AuthorsMathieu, M. / Petitpas, I. / Rey, F.A.
Citation
Journal: EMBO J. / Year: 2001
Title: Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion.
Authors: Mathieu, M. / Petitpas, I. / Navaza, J. / Lepault, J. / Kohli, E. / Pothier, P. / Prasad, B.V. / Cohen, J. / Rey, F.A.
#1: Journal: J.Virol. / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Rotavirus Protein Vp6
Authors: Petitpas, I. / Lepault, J. / Vachette, P. / Charpilienne, A. / Mathieu, M. / Kohli, E. / Pothier, P. / Cohen, J. / Rey, F.A.
History
DepositionApr 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 13, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIRAL CAPSID VP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2078
Polymers44,9061
Non-polymers3017
Water5,224290
1
A: VIRAL CAPSID VP6
hetero molecules

A: VIRAL CAPSID VP6
hetero molecules

A: VIRAL CAPSID VP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,62124
Polymers134,7173
Non-polymers90421
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15230 Å2
ΔGint-186 kcal/mol
Surface area40510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.780, 157.780, 157.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Cell settingcubic
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-501-

ZN

21A-502-

CL

31A-503-

CA

41A-508-

CA

51A-890-

HOH

61A-891-

HOH

71A-892-

HOH

81A-893-

HOH

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Components

#1: Protein VIRAL CAPSID VP6


Mass: 44905.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ONE MONOMER IN ASYMETRIC UNIT / Source: (gene. exp.) Bovine rotavirus / Species: Rotavirus A / Strain: RF / Gene: SEGMENT 6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04509
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-ACETYLATION IN THE STRUCTURE, NUMBERED AS RESIDUE ACE A 0 ERROR IN CDNA SEQUENCING GLN142 WRITTEN ...N-ACETYLATION IN THE STRUCTURE, NUMBERED AS RESIDUE ACE A 0 ERROR IN CDNA SEQUENCING GLN142 WRITTEN AS PRO IN DATABASE (UNDER CORRECTION)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66.2 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES PH 7.5, 200MM CACL2, 14 TO 20% PEG 550, pH 7.5, vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: unknown / Details: Petitpas, I., (1998) J.Virol., 72, 7615.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein11
2100 mM11Ca2+
314-20 %mPEG55011
4200 mM11CaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1110.88
SYNCHROTRONEMBL/DESY, HAMBURG BW7B20.88
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEAug 15, 1998
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.95→42 Å / Num. obs: 48534 / % possible obs: 98.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 28.11 Å2 / Rsym value: 7.2 / Net I/σ(I): 15.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.1 / Rsym value: 25.2 / % possible all: 97.3
Reflection
*PLUS
Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.95→42 Å / Rfactor Rfree error: 0.0044 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2444 5 %RANDOM
Rwork0.188 ---
obs-48467 98.3 %-
Displacement parametersBiso mean: 27.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.252 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.209 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 7 290 3459
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.629
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.94
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.425
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.3671
X-RAY DIFFRACTIONx_mcangle_it2.2971
X-RAY DIFFRACTIONx_scbond_it3.8762
X-RAY DIFFRACTIONx_scangle_it6.012
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 266 5.52 %
Rwork0.269 4432 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.ION
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.216 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.425

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