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- PDB-1qgt: HUMAN HEPATITIS B VIRAL CAPSID (HBCAG) -

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Basic information

Entry
Database: PDB / ID: 1qgt
TitleHUMAN HEPATITIS B VIRAL CAPSID (HBCAG)
ComponentsPROTEIN (HBV CAPSID PROTEIN)
KeywordsVIRUS / VIRAL CAPSID PROTEIN / Icosahedral virus
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / viral envelope / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.3 Å
AuthorsLeslie, A.G.W. / Wynne, S.A. / Crowther, R.A.
Citation
Journal: Mol.Cell / Year: 1999
Title: The crystal structure of the human hepatitis B virus capsid.
Authors: Wynne, S.A. / Crowther, R.A. / Leslie, A.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization of Hepatitis B Virus Core Protein Shells: Determination of Cryoprotectant Conditions and Preliminary X-Ray Characterization
Authors: Wynne, S.A. / Leslie, A.G.W. / Butler, P.J.G. / Crowther, R.A.
History
DepositionMay 5, 1999Deposition site: PDBE / Processing site: NDB
Revision 1.0Jun 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: PROTEIN (HBV CAPSID PROTEIN)
D: PROTEIN (HBV CAPSID PROTEIN)
B: PROTEIN (HBV CAPSID PROTEIN)
A: PROTEIN (HBV CAPSID PROTEIN)


Theoretical massNumber of molelcules
Total (without water)67,4654
Polymers67,4654
Non-polymers00
Water00
1
C: PROTEIN (HBV CAPSID PROTEIN)
D: PROTEIN (HBV CAPSID PROTEIN)
B: PROTEIN (HBV CAPSID PROTEIN)
A: PROTEIN (HBV CAPSID PROTEIN)
x 60


Theoretical massNumber of molelcules
Total (without water)4,047,908240
Polymers4,047,908240
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
C: PROTEIN (HBV CAPSID PROTEIN)
D: PROTEIN (HBV CAPSID PROTEIN)
B: PROTEIN (HBV CAPSID PROTEIN)
A: PROTEIN (HBV CAPSID PROTEIN)
x 5


  • icosahedral pentamer
  • 337 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)337,32620
Polymers337,32620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: PROTEIN (HBV CAPSID PROTEIN)
D: PROTEIN (HBV CAPSID PROTEIN)
B: PROTEIN (HBV CAPSID PROTEIN)
A: PROTEIN (HBV CAPSID PROTEIN)
x 6


  • icosahedral 23 hexamer
  • 405 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)404,79124
Polymers404,79124
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
C: PROTEIN (HBV CAPSID PROTEIN)
D: PROTEIN (HBV CAPSID PROTEIN)
B: PROTEIN (HBV CAPSID PROTEIN)
A: PROTEIN (HBV CAPSID PROTEIN)
x 30


  • crystal asymmetric unit, crystal frame
  • 2.02 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,023,954120
Polymers2,023,954120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)538.400, 354.800, 370.100
Angle α, β, γ (deg.)90.00, 132.30, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.4589297, -0.50775021, 0.72909071), (0.84616288, 0.50000004, -0.18441348), (-0.2709094, 0.70156232, 0.65910425)
3generate(-0.41654043, 0.02460579, 0.90878415), (0.8613701, -0.30901689, 0.40317504), (0.29075009, 0.9507382, 0.10752333)
4generate(-0.41654043, 0.8613701, 0.29075009), (0.02460579, -0.30901689, 0.9507382), (0.90878415, 0.40317504, 0.10752333)
5generate(0.4589297, 0.84616288, -0.2709094), (-0.50775021, 0.50000004, 0.70156232), (0.72909071, -0.18441348, 0.65910425)
6generate(0.48391682, 0.53235611, 0.69456568), (0.5323561, -0.80901691, 0.24917588), (0.69456568, 0.24917588, -0.67489991)
7generate(0.48437941, 0.50775032, 0.71243681), (-0.50775014, -0.5, 0.7015624), (0.71243693, -0.70156227, 0.01562059)
8generate(0.45892974, 0.50775025, 0.72909065), (-0.84616291, 0.49999996, 0.18441359), (-0.27090925, -0.70156234, 0.65910429)
9generate(0.4427384, 0.532356, 0.72151216), (-0.01520726, 0.80901701, -0.58758847), (-0.89652186, 0.24917576, 0.36627857)
10generate(0.45818126, 0.54756325, 0.70017456), (0.83676435, 1.0E-7, -0.54756317), (-0.29982554, 0.83676429, -0.45818136)
11generate(-0.99953748, -0.02460585, 0.01787121), (-0.02460585, 0.30901692, -0.95073818), (0.01787121, -0.95073818, -0.30947944)
12generate(-0.48437947, 0.5077502, -0.71243684), (0.5077502, -0.49999999, -0.70156236), (-0.71243684, -0.70156236, -0.01562054)
13generate(0.40034909, 6.0E-8, -0.91636271), (6.0E-8, -1, -4.0E-8), (-0.91636271, -4.0E-8, -0.40034909)
14generate(0.4319834, -0.84616285, -0.31208776), (-0.84616285, -0.50000009, 0.1844135), (-0.31208776, 0.1844135, -0.93198331)
15generate(-0.43319407, -0.86137014, 0.26530055), (-0.86137014, 0.30901686, -0.40317499), (0.26530055, -0.40317499, -0.87582278)
16generate(-0.44273847, 0.01520715, 0.89652183), (0.53235589, 0.80901706, 0.24917584), (-0.7215122, 0.58758841, -0.36627859)
17generate(-0.43319429, 0.86137006, 0.26530044), (0.86137006, 0.30901713, 0.40317494), (0.26530044, 0.40317494, -0.87582284)
18generate(0.45818126, 0.83676435, -0.29982554), (0.54756325, 1.0E-7, 0.83676429), (0.70017456, -0.54756317, -0.45818136)
19generate(0.99953748, -0.02460572, -0.01787121), (0.02460581, 0.30901699, 0.95073816), (-0.01787109, -0.95073816, 0.30947951)
20generate(0.44273847, -0.53235599, 0.72151212), (0.01520714, 0.80901697, 0.58758853), (-0.89652183, -0.2491759, 0.36627855)
21generate(0.45818144, -0.83676431, -0.29982537), (-0.54756314, -1.0E-7, -0.83676437), (0.70017453, 0.54756323, -0.45818134)
22generate(-0.41654032, -0.86137009, 0.29075027), (-0.02460574, -0.3090171, -0.95073813), (0.9087842, -0.40317489, 0.10752343)
23generate(-0.99878911, -0.01520721, 0.04678732), (-0.01520721, -0.80901704, -0.58758844), (0.04678732, -0.58758844, 0.80780615)
24generate(-0.48391689, 0.53235599, -0.69456572), (-0.532356, -0.80901699, -0.24917582), (-0.69456571, 0.24917584, 0.6748999)
25generate(0.41654043, 0.02460578, -0.90878415), (-0.86137006, -0.30901703, -0.40317501), (-0.29075021, 0.95073815, -0.1075234)
26generate(-0.4319833, -0.84616288, 0.31208782), (0.84616291, -0.5, -0.18441346), (0.31208774, 0.18441361, 0.9319833)
27generate(-0.99878911, 0.01520719, 0.04678725), (0.01520719, -0.80901695, 0.58758856), (0.04678725, 0.58758856, 0.80780606)
28generate(-0.45818133, 0.54756314, -0.7001746), (-0.83676435, 3.0E-8, 0.54756317), (0.29982543, 0.83676437, 0.4581813)
29generate(0.44273847, 0.01520714, -0.89652183), (-0.53235599, 0.80901697, -0.2491759), (0.72151212, 0.58758853, 0.36627855)
30generate(0.45892974, -0.84616291, -0.27090925), (0.50775025, 0.49999996, -0.70156234), (0.72909065, 0.18441359, 0.65910429)

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Components

#1: Protein
PROTEIN (HBV CAPSID PROTEIN) / HBCAG


Mass: 16866.283 Da / Num. of mol.: 4 / Fragment: ASSEMBLY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Genus: Orthohepadnavirus / Strain: ISOLATED AT ST MARY'S HOSPITAL, LONDON / Description: THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 149 / Plasmid: PT7-SC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q67855
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

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Sample preparation

CrystalDensity % sol: 82 %
Crystal growpH: 6.5
Details: EQUAL VOLUMES OF PROTEIN (15MG/ML) IN 5MM TRIS-HCL, 150MM NACL PH7.5 AND 0.1M MES, PH 6.5, 0.1-0.4M (NH4)2SO4, 3.5-4% PEG20000 AND 20% BUTANEDIOL. HANGING DROP
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
25 mMTris-HCl1drop
3150 mM1dropNaCl
40.1 MMES1reservoir
50.1-0.4 Mammonium sulfate1reservoir
63.5-4 %PEG200001reservoir
720 %butanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99188
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 3.3→38.8 Å / Num. obs: 727106 / % possible obs: 94.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 6.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 0.9 / % possible all: 78.2
Reflection shell
*PLUS
% possible obs: 78.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4SCALAdata reduction
CCP4model building
SOLOMONphasing
SIGMAAmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
CCP4phasing
SIGMAAphasing
RefinementMethod to determine structure: OTHER / Resolution: 3.3→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP B'S / σ(F): 0 / Details: STRICT ICOSAHEDRAL SYMMETRY IMPOSED
RfactorNum. reflection% reflection
Rwork0.271 --
obs-649882 94.2 %
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 3.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 0 0 4560
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_deg2.02
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.9
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.3→3.44 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.448 59490
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9

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