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- PDB-2g33: Human Hepatitis B Virus T=4 capsid, strain adyw -

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Basic information

Entry
Database: PDB / ID: 2g33
TitleHuman Hepatitis B Virus T=4 capsid, strain adyw
ComponentsCore antigen
KeywordsVIRUS / capsid / hepadnavirus / four-helix bundle / icosahedral
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 / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein 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 subtype adyw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 Å
AuthorsBourne, C.R. / Zlotnick, A.
CitationJournal: J.Virol. / Year: 2006
Title: Global Structural Changes in Hepatitis B Virus Capsids Induced by the Assembly Effector HAP1.
Authors: Bourne, C.R. / Finn, M.G. / Zlotnick, A.
History
DepositionFeb 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen


Theoretical massNumber of molelcules
Total (without water)67,1644
Polymers67,1644
Non-polymers00
Water00
1
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 60


Theoretical massNumber of molelcules
Total (without water)4,029,865240
Polymers4,029,865240
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: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 5


  • icosahedral pentamer
  • 336 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)335,82220
Polymers335,82220
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 6


  • icosahedral 23 hexamer
  • 403 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)402,98624
Polymers402,98624
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: Core antigen
D: Core antigen
B: Core antigen
A: Core antigen
x 60


  • crystal asymmetric unit, crystal frame
  • 4.03 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,029,865240
Polymers4,029,865240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)558.400, 327.145, 562.237
Angle α, β, γ (deg.)90.00, 109.12, 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:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.447239, 0.347018, 0.824315), (0.203815, 0.85788, -0.471643), (-0.870927, 0.379041, 0.312911)-57.524719, 43.58379, 174.303477
3generate(-0.44717, 0.765352, 0.462935), (0.676773, 0.627918, -0.384189), (-0.584781, 0.141557, -0.798782)75.553458, -12.960152, 295.465578
4generate(-0.447185, 0.676882, -0.584725), (0.765262, 0.627907, 0.141504), (0.462997, -0.384264, -0.798756)215.32506, -91.490006, 196.043853
5generate(0.447215, 0.203868, -0.870835), (0.346993, 0.857867, 0.378947), (0.824412, -0.471751, 0.312952)168.630503, -83.480299, 13.436082
6generate(-0.471693, 0.097649, 0.876298), (-0.481892, 0.803825, -0.348839), (-0.738475, -0.586833, -0.332132)21.614648, 91.624443, 246.470518
7generate(-0.95425, 0.252243, -0.160677), (0.252126, 0.390138, -0.885504), (-0.160617, -0.885591, -0.435888)205.746603, 93.574785, 205.482901
8generate(-0.235429, -0.175648, -0.95585), (0.96349, 0.086539, -0.253259), (0.127296, -0.980693, 0.14889)243.626923, -58.271845, 100.148122
9generate(0.691385, -0.594695, -0.41032), (0.669119, 0.31259, 0.674156), (-0.272622, -0.740711, 0.614058)82.906184, -154.068553, 76.035287
10generate(0.545367, -0.425788, 0.72201), (-0.224176, 0.755898, 0.615084), (-0.807698, -0.497293, 0.31677)-54.30502, -61.427526, 166.46761
11generate(-0.471686, -0.481809, -0.738454), (0.097557, 0.803788, -0.586825), (0.876394, -0.348916, -0.332102)236.34784, 68.879878, 94.879777
12generate(0.333985, -0.856926, -0.392646), (0.71854, 0.500979, -0.482307), (0.610081, -0.121089, 0.783071)113.767072, -3.985885, -28.628433
13generate(0.316683, -0.768076, 0.556609), (0.843523, 0.49631, 0.205101), (-0.433827, 0.404648, 0.805041)-11.233091, -107.553197, 67.491548
14generate(-0.499681, -0.338045, 0.797474), (0.299785, 0.796232, 0.525424), (-0.812685, 0.501742, -0.296555)34.09322, -98.695594, 250.405249
15generate(-0.98692, -0.161122, -0.002919), (-0.161248, 0.986267, 0.035988), (-0.002924, 0.036014, -0.999348)187.106625, 10.345966, 267.332031
16generate(-0.789356, 0.538714, 0.294539), (0.538635, 0.377535, 0.75316), (0.294521, 0.753224, -0.588179)129.886877, -152.239005, 185.555224
17generate(-0.499755, 0.299878, -0.812594), (-0.338103, 0.796278, 0.501615), (0.797503, 0.525435, -0.296523)250.11278, -35.490715, 98.919526
18generate(0.545322, -0.224173, -0.80766), (-0.42579, 0.755922, -0.497303), (0.722017, 0.615115, 0.31679)150.292601, 106.096774, 24.258877
19generate(0.901615, -0.309219, 0.302522), (0.396754, 0.312237, -0.863121), (0.172383, 0.898326, 0.404182)-31.625573, 76.854295, 64.751646
20generate(0.076739, 0.162271, 0.983718), (0.992802, 0.078381, -0.090293), (-0.091824, 0.983683, -0.155119)-44.236929, -82.80586, 164.438328
21generate(-0.104776, 0.183107, -0.97746), (-0.99219, -0.08591, 0.090157), (-0.06754, 0.979382, 0.190687)234.779461, 79.626631, 115.966154
22generate(0.841759, -0.249778, -0.478588), (-0.539777, -0.383833, -0.749148), (0.003332, 0.889038, -0.457926)78.412198, 148.672569, 195.773963
23generate(0.742375, -0.103583, 0.661926), (0.332814, -0.800557, -0.49833), (0.581512, 0.590274, -0.559852)-64.315693, 32.414943, 154.511735
24generate(-0.265583, 0.419655, 0.86793), (0.419692, -0.760184, 0.495989), (0.867974, 0.495971, 0.025767)3.840899, -108.482384, 49.202327
25generate(-0.789152, 0.596837, -0.145268), (-0.399206, -0.318507, 0.859693), (0.466838, 0.736454, 0.489625)188.692083, -79.303779, 25.379872
26generate(0.683015, 0.71056, 0.168956), (0.44283, -0.21885, -0.869429), (-0.580915, 0.668755, -0.464165)8.376532, 72.53032, 251.240222
27generate(0.303147, 0.910638, 0.280757), (0.910659, -0.363633, 0.196197), (0.280751, 0.196188, -0.939514)29.504707, -114.026637, 232.898371
28generate(0.076661, 0.992838, -0.091756), (0.162294, 0.078426, 0.983567), (0.983799, -0.090387, -0.155088)100.692361, -148.062587, 61.538166
29generate(0.316555, 0.843563, -0.433784), (-0.768048, 0.496416, 0.404561), (0.556642, 0.205067, 0.805063)123.560587, 17.459002, -26.02654
30generate(0.691303, 0.669105, -0.272656), (-0.594668, 0.312689, -0.740655), (-0.410404, 0.674244, 0.614042)66.506324, 153.793063, 91.215893
31generate(0.191954, -0.293131, -0.936566), (0.487989, -0.799564, 0.350153), (-0.851517, -0.524251, -0.010424)200.651141, -95.495155, 214.243593
32generate(0.841788, -0.539862, 0.003423), (-0.249674, -0.383868, 0.888932), (-0.478603, -0.749189, -0.45792)13.586204, -97.381663, 238.560947
33generate(0.263468, -0.169728, 0.949593), (-0.9641, -0.07901, 0.253395), (0.032069, -0.982373, -0.184458)-57.77014, 55.194679, 153.622885
34generate(-0.743788, 0.305759, 0.594369), (-0.667977, -0.306292, -0.678169), (-0.025231, -0.901552, 0.432046)85.19415, 151.378627, 76.810927
35generate(0.683018, 0.442806, -0.580806), (0.710611, -0.218883, 0.668653), (0.169011, -0.869545, -0.464135)108.083655, -158.069327, 178.26228
36generate(0.901565, 0.396744, 0.172435), (-0.309148, 0.312268, 0.898231), (0.30259, -0.863248, 0.404201)-13.144432, -91.938031, 49.741359
37generate(0.333899, 0.718579, 0.610009), (-0.856915, 0.50108, -0.121049), (-0.392645, -0.482353, 0.783055)-17.659073, 96.020487, 65.1651
38generate(-0.235484, 0.963548, 0.127203), (-0.175693, 0.086622, -0.980576), (-0.955903, -0.253243, 0.148862)100.778744, 146.053983, 203.218464
39generate(-0.019717, 0.793112, -0.608761), (0.793092, -0.358339, -0.492513), (-0.60878, -0.492542, -0.621944)178.491957, -10.982289, 273.116413
40generate(-0.106649, 0.763472, 0.636964), (-0.723495, -0.498941, 0.476981), (0.682057, -0.410088, 0.60559)20.267123, 2.038429, -12.151865
41generate(-0.446841, 0.8594, -0.248687), (-0.840685, -0.498301, -0.211814), (-0.305966, 0.114423, 0.945141)170.702296, 105.051279, 36.296347
42generate(0.191904, 0.487941, -0.851485), (-0.293075, -0.799502, -0.524248), (-0.93667, 0.350236, -0.010435)190.515498, 94.773736, 223.625754
43generate(0.92686, 0.162438, -0.338384), (0.162557, -0.986296, -0.028547), (-0.338445, -0.028531, -0.940564)52.325572, -14.591079, 290.953399
44generate(0.742344, 0.332726, 0.581528), (-0.103458, -0.800538, 0.590246), (0.661984, -0.49844, -0.55984)-52.89373, -71.904591, 145.234869
45generate(0.577342, -0.768206, 0.276803), (-0.7681, -0.625916, -0.134792), (0.276796, -0.134807, -0.951426)1.605148, 87.735557, 234.343652
46generate(-0.139439, -0.353763, 0.924846), (-0.353702, -0.854598, -0.380124), (0.924944, -0.38023, -0.005963)-16.839796, 81.145774, 46.708424
47generate(-0.93994, -0.001316, 0.341303), (-0.00131, -0.999972, -0.007441), (0.341368, -0.007482, 0.939912)136.967102, -2.011196, -24.109969
48generate(-0.717898, -0.197935, -0.667389), (-0.197915, -0.861135, 0.468222), (-0.667449, 0.46831, 0.579032)250.470064, -46.815333, 119.757017
49generate(0.219834, -0.671899, -0.707252), (-0.671818, -0.629956, 0.389515), (-0.707357, 0.38962, -0.589879)166.811687, 8.651168, 279.490063
50generate(-0.106549, -0.723562, 0.681969), (0.763471, -0.499031, -0.40997), (0.637003, 0.476996, 0.60558)11.921646, -19.438111, -6.523552
51generate(-0.789073, -0.39921, 0.466829), (0.596799, -0.318572, 0.736421), (-0.145305, 0.859801, 0.489612)105.385018, -156.565607, 83.177202
52generate(-0.840845, -0.439348, -0.316085), (-0.439389, 0.212938, 0.872637), (-0.316163, 0.872772, -0.372092)214.747254, -76.41995, 214.350443
53generate(-0.190318, -0.788508, -0.584813), (-0.913118, 0.360971, -0.189569), (0.36055, 0.497983, -0.788687)188.873584, 110.240589, 205.719322
54generate(0.263503, -0.964161, 0.032019), (-0.169709, -0.079051, -0.982264), (0.94964, 0.253381, -0.184451)63.52032, 145.457152, 69.211447
55generate(-0.10468, -0.992224, -0.067465), (0.183109, -0.085998, 0.979274), (-0.977535, 0.090249, 0.190677)111.407854, -149.705161, 200.207175
56generate(-0.190291, -0.913112, 0.360576), (-0.788514, 0.360956, 0.497924), (-0.584865, -0.189522, -0.788699)62.425266, 6.704801, 293.609057
57generate(-0.585248, -0.712703, 0.386632), (-0.712743, 0.224767, -0.66442), (0.386699, -0.664498, -0.639519)96.424612, 154.585648, 181.520019
58generate(-0.743735, -0.667956, -0.025307), (0.305707, -0.306355, -0.901439), (0.594488, -0.678279, 0.432056)166.420077, 89.571323, 18.843314
59generate(-0.446728, -0.84071, -0.305954), (0.859374, -0.498418, 0.11442), (-0.248656, -0.211818, 0.945146)175.680192, -98.490803, 30.392607
60generate(-0.787986, 0.229492, -0.571342), (0.229464, -0.751618, -0.618369), (-0.571317, -0.618417, 0.539605)244.907386, 58.247084, 114.276524

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Components

#1: Protein
Core antigen


Mass: 16791.104 Da / Num. of mol.: 4 / Fragment: Assembly domain residues 1 to 149 / Mutation: C48A, C61A, C107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus subtype adyw / Genus: Orthohepadnavirus / Species: Hepatitis B virus / Strain: adyw / Gene: C / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Gold / References: UniProt: P03147

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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: 6.3 Å3/Da / Density % sol: 80.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 5000 MME, butanediol, KCl, NaCl, bicarbonate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.95→40 Å / Num. all: 824879 / Num. obs: 666347 / % possible obs: 81.1 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.061 / Χ2: 1.068 / Net I/σ(I): 10.5
Reflection shellResolution: 3.95→4.02 Å / % possible obs: 64.6 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.3 / Num. unique all: 26503 / Num. unique obs: 26503 / Rsym value: 0.482 / Χ2: 1.141 / % possible all: 64.6

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Phasing

Phasing MRRfactor: 0.672 / Cor.coef. Fo:Fc: 0.148
Highest resolutionLowest resolution
Rotation3 Å40 Å
Translation3 Å40 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QGT

1qgt


Resolution: 3.96→40 Å / Cross valid method: Not applicable / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement was limited to positional refinement and grouped B-factor refinement. This was alternated with 60-fold NCS averaging with RAVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.372 6675 0.8 %Selected as thin shells; due to 60-fold NCS R-free is not applicable
Rwork0.36 ---
all-821636 --
obs-653450 79.2 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 106.159 Å2
Refine analyzeLuzzati coordinate error obs: 1.08 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.46 Å
Refinement stepCycle: LAST / Resolution: 3.96→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 0 0 4658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.99
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.96-4.140.4734450.485216252607
4.14-4.360.5068900.4847020471094
4.36-4.630.58900.4747611777007
4.63-4.990.4518900.4448405184941
4.99-5.490.4378900.428996290852
5.49-6.280.3948900.3979271693606
6.28-7.90.3738900.3419260093490
7.9-400.2438900.2498896389853
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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