[English] 日本語
Yorodumi
- PDB-2g34: Human hepatitis B virus T=4 capsid strain adyw complexed with ass... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g34
TitleHuman hepatitis B virus T=4 capsid strain adyw complexed with assembly effector HAP1
ComponentsCore antigenHepatitis B virus
KeywordsVIRUS / capsid / hepadnavirus / four-helix bundle / icosahedral / assembly misdirector / assembly activator
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 cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus subtype
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.053 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: Source and taxonomy / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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)528.530, 366.470, 540.070
Angle α, β, γ (deg.)90.00, 104.83, 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(0.559015, -0.4229, 0.713158), (0.810743, 0.459314, -0.363308), (-0.173835, 0.780974, 0.599701)-50.81488, -31.215766, 69.575869
3generate(-0.154339, 0.126305, 0.979993), (0.888762, -0.415632, 0.193441), (0.43175, 0.900585, -0.048062)-16.40146, -112.029519, 95.754422
4generate(-0.154234, 0.888637, 0.431749), (0.126234, -0.415694, 0.900837), (0.979856, 0.193528, -0.048106)55.682091, -130.758648, 42.358242
5generate(0.559187, 0.810577, -0.173919), (-0.423051, 0.459214, 0.781284), (0.71302, -0.363065, 0.599632)65.818696, -61.520651, -16.821288
6generate(-0.361397, 0.162022, 0.918355), (0.665767, 0.734299, 0.132243), (-0.65278, 0.659285, -0.372902)11.879201, -82.259662, 244.147738
7generate(-0.230309, 0.944471, 0.234144), (0.944516, 0.158998, 0.287327), (0.234422, 0.287653, -0.928688)89.08081, -129.811771, 230.793411
8generate(0.596277, 0.714071, -0.366962), (0.606959, -0.102013, 0.788135), (0.525698, -0.692299, -0.494264)87.591785, -162.779668, 145.287726
9generate(0.976049, -0.210775, -0.054256), (0.119588, 0.311975, 0.942566), (-0.181485, -0.926312, 0.33001)9.469943, -135.60279, 105.796852
10generate(0.384174, -0.55196, 0.740115), (0.155934, 0.828845, 0.537203), (-0.909824, -0.090987, 0.405015)-37.323184, -85.838757, 166.895746
11generate(-0.361007, 0.665876, -0.652922), (0.161941, 0.73425, 0.659203), (0.918266, 0.132499, -0.373243)218.472635, -102.467501, 91.11751
12generate(0.451548, -0.051399, -0.890931), (0.571225, 0.783591, 0.244058), (0.685631, -0.618974, 0.382896)170.603529, -87.752619, 14.351076
13generate(0.365625, -0.910368, -0.193596), (0.912192, 0.308945, 0.269052), (-0.185112, -0.275226, 0.943464)87.275733, -124.259633, 25.473064
14generate(-0.500033, -0.723964, 0.475391), (0.713636, -0.033744, 0.699644), (-0.490625, 0.688693, 0.533774)83.645213, -161.537018, 109.11328
15generate(-0.949117, 0.250209, 0.191513), (0.249955, 0.22911, 0.940772), (0.1913, 0.940682, -0.279993)164.729284, -148.068895, 149.683523
16generate(-0.931219, 0.100709, 0.350535), (0.100631, -0.852657, 0.512854), (0.350027, 0.512509, 0.783876)142.073672, -77.239169, -5.6865
17generate(-0.499852, 0.713834, -0.490477), (-0.724185, -0.033666, 0.689102), (0.474921, 0.699565, 0.533519)210.638322, -20.053797, 15.066969
18generate(0.384574, 0.156212, -0.909954), (-0.551916, 0.82897, -0.090971), (0.739914, 0.537142, 0.40449)179.629881, 65.74116, 6.215957
19generate(0.499812, -0.801542, -0.328194), (0.379368, 0.54312, -0.749328), (0.778795, 0.249702, 0.575103)91.90091, 61.579957, -20.00773
20generate(-0.313393, -0.835844, 0.450831), (0.782664, -0.496183, -0.376144), (0.537832, 0.234479, 0.809575)68.689965, -26.786682, -27.363758
21generate(0.174767, 0.154175, -0.972586), (-0.938819, -0.271683, -0.211588), (-0.296984, 0.949844, 0.096916)208.309397, 119.307898, 147.694047
22generate(0.391763, -0.762665, -0.514641), (-0.7083, 0.106997, -0.697711), (0.587216, 0.637563, -0.49876)126.947784, 160.77341, 139.87769
23generate(-0.309863, -0.917905, 0.247838), (-0.187917, -0.196209, -0.962421), (0.931867, -0.345015, -0.111962)95.041605, 144.881853, 55.434545
24generate(-0.960489, -0.097008, 0.26113), (-0.096823, -0.762282, -0.639898), (0.260672, -0.640001, 0.72277)156.684108, 93.594783, 11.06205
25generate(-0.660971, 0.565573, -0.493136), (-0.560905, -0.808927, -0.175857), (-0.4988, 0.160267, 0.851864)226.687755, 77.789134, 68.081655
26generate(0.674369, -0.499685, 0.543567), (0.296529, -0.491102, -0.819197), (0.67644, 0.713247, -0.183267)-39.751754, 78.845468, 89.693995
27generate(-0.122625, -0.090193, 0.98845), (-0.08999, -0.99075, -0.101383), (0.988262, -0.101592, 0.113375)-20.602542, 22.111756, 20.304841
28generate(-0.3135, 0.782389, 0.538093), (-0.835927, -0.496186, 0.234969), (0.45038, -0.37606, 0.809686)57.216059, 50.558162, -18.853974
29generate(0.365528, 0.912183, -0.185125), (-0.910424, 0.309117, -0.274968), (-0.19387, 0.26915, 0.943388)86.16138, 124.872919, 26.333461
30generate(0.976066, 0.119816, -0.181744), (-0.210528, 0.31226, -0.926479), (-0.054157, 0.942379, 0.329709)26.232035, 142.355506, 93.419886
31generate(0.937312, -0.221226, -0.269531), (-0.017029, -0.800988, 0.598625), (-0.347807, -0.556426, -0.754357)41.554598, -77.054425, 264.602799
32generate(0.391468, -0.708502, 0.587185), (-0.762979, 0.106809, 0.637857), (-0.514416, -0.697623, -0.498278)-17.921768, -9.53565, 247.161166
33generate(-0.457651, -0.032401, 0.888719), (-0.450804, 0.869879, -0.200403), (-0.766544, -0.492024, -0.412228)25.156314, 70.280163, 260.41038
34generate(-0.436593, 0.872731, 0.218362), (0.488081, 0.433684, -0.75771), (-0.755758, -0.22376, -0.615126)111.25632, 52.090205, 286.040474
35generate(0.674293, 0.296121, 0.676287), (-0.499793, -0.49128, 0.713626), (0.543699, -0.819, -0.183013)-57.202276, -45.140486, 102.602716
36generate(0.499458, 0.379018, 0.778866), (-0.801748, 0.543039, 0.250017), (-0.32825, -0.74904, 0.575538)-53.657248, 45.243294, 87.807613
37generate(0.451099, 0.571144, 0.685581), (-0.051386, 0.783746, -0.619126), (-0.890828, 0.244255, 0.383189)-36.678628, 86.427544, 167.913259
38generate(0.596047, 0.606987, 0.525349), (0.714319, -0.101807, -0.692679), (-0.366569, 0.788187, -0.49424)-29.730396, 21.497122, 232.216255
39generate(0.733988, 0.437015, 0.519606), (0.437188, -0.889817, 0.131007), (0.520017, 0.131059, -0.844171)-42.414926, -59.81642, 191.85211
40generate(-0.488007, 0.772558, 0.406212), (-0.612294, 0.028758, -0.790069), (-0.622287, -0.633957, 0.459249)91.562859, 163.565013, 131.749782
41generate(0.282931, 0.878471, -0.385094), (-0.181626, -0.344876, -0.920917), (-0.941681, 0.330645, 0.061945)120.506888, 138.811486, 215.113597
42generate(0.937322, -0.016908, -0.348321), (-0.221052, -0.800812, -0.556508), (-0.269114, 0.598488, -0.754544)51.913917, 94.733159, 256.953493
43generate(0.57082, -0.676196, 0.465711), (-0.676087, -0.708963, -0.200444), (0.465948, -0.200578, -0.861857)-19.422655, 92.244879, 199.448009
44generate(-0.310082, -0.188278, 0.932039), (-0.917888, -0.196259, -0.344792), (0.247675, -0.962272, -0.111693)5.081576, 134.785229, 122.068049
45generate(-0.494322, -0.85674, 0.146941), (-0.8568, 0.451626, -0.248972), (0.146937, -0.248946, -0.957303)126.283009, 116.228446, 243.083612
46generate(-0.996476, -0.069704, 0.046851), (-0.069532, 0.375341, -0.92442), (0.04672, -0.924118, -0.378864)188.369659, 128.346144, 176.783262
47generate(-0.621703, 0.425987, -0.657223), (0.426132, -0.520148, -0.740329), (-0.657248, -0.740103, 0.14185)244.441009, 55.845803, 176.897014
48generate(0.112073, -0.054695, -0.992275), (-0.054798, -0.997305, 0.048895), (-0.992107, 0.048794, -0.114769)217.008406, -1.079819, 243.267624
49generate(0.190798, -0.847464, -0.495274), (-0.847694, -0.396716, 0.35257), (-0.495094, 0.352346, -0.794082)143.98274, 36.238782, 284.173088
50generate(-0.487663, -0.612318, -0.622056), (0.772846, 0.028664, -0.63428), (0.406065, -0.790129, 0.458999)226.761399, 8.113904, 31.584015
51generate(-0.660911, -0.560825, -0.498371), (0.565532, -0.809033, 0.160366), (-0.493387, -0.176176, 0.85191)227.376413, -76.183265, 67.549936
52generate(-0.737513, -0.36731, -0.566457), (-0.367656, -0.485524, 0.793412), (-0.566737, 0.793058, 0.223037)243.792958, -68.508076, 157.392986
53generate(-0.611607, -0.299204, -0.732222), (-0.737085, 0.552114, 0.39001), (0.287383, 0.778126, -0.558541)253.324066, 20.53254, 176.953359
54generate(-0.457191, -0.450628, -0.766585), (-0.032216, 0.869898, -0.492353), (0.888607, -0.200339, -0.412706)242.798023, 67.887698, 99.198857
55generate(0.174645, -0.938749, -0.296857), (0.153825, -0.271906, 0.950062), (-0.972417, -0.21179, 0.097261)119.463929, -139.921338, 213.467059
56generate(-0.611854, -0.736878, 0.287576), (-0.299609, 0.552036, 0.778242), (-0.732213, 0.389921, -0.558215)119.239792, -73.148967, 276.258854
57generate(-0.989447, 0.144888, 0.003826), (0.144788, 0.988054, 0.052488), (0.003845, 0.052798, -0.998606)193.341777, -21.010158, 262.456014
58generate(-0.436315, 0.487978, -0.755976), (0.872875, 0.433588, -0.224233), (0.218547, -0.757265, -0.615307)239.36378, -55.559021, 191.133915
59generate(0.283133, -0.181747, -0.941809), (0.878461, -0.34511, 0.330499), (-0.384817, -0.920789, 0.061977)193.704825, -129.050186, 160.857057
60generate(0.425542, 0.756031, -0.497476), (0.756169, -0.598969, -0.263883), (-0.496964, -0.263563, -0.826573)121.391039, -38.967623, 288.631403

-
Components

#1: Protein
Core antigen / Hepatitis B virus


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 / 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 6.6 Å3/Da / Density % sol: 81.1 %
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

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5→25 Å / Num. all: 411133 / Num. obs: 407824 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Χ2: 1.086 / Net I/σ(I): 7.4
Reflection shellResolution: 5→5.09 Å / % possible obs: 82.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.66 / Num. unique obs: 17315 / Χ2: 1.13 / % possible all: 87.5

-
Phasing

Phasing MRRfactor: 0.465 / Cor.coef. Fo:Fc: 0.746
Highest resolutionLowest resolution
Translation3 Å25.03 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 2G33

2g33


Resolution: 5.053→25.031 Å / 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. Putative density for the small molecule HAP1 was ...Details: Refinement was limited to positional refinement and grouped B-factor refinement. This was alternated with 60-fold NCS averaging with RAVE. Putative density for the small molecule HAP1 was identified close to C102, but was not modelled into the density and is not included in the deposition.
RfactorNum. reflection% reflectionSelection details
Rwork0.365 ---
Rfree-5175 1.3 %Reflections were selected in thin shells; however, 60-fold NCS results in R-free being not applicable.
all-411133 --
obs-397911 96.8 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 135.195 Å2
Refine analyzeLuzzati coordinate error obs: 1.27 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 2.09 Å
Refinement stepCycle: LAST / Resolution: 5.053→25.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 0 0 4622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d1.3
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
5.05-5.280.5076900.4874335044040
5.28-5.560.5173450.4654754247887
5.56-5.90.486900.4534881849508
5.9-6.350.4586900.4385009050780
6.35-6.980.4196900.4195049251182
6.98-7.960.3886900.3925066251352
7.96-9.920.2966900.3145074751437
9.92-25.030.2856900.2865103551725
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2DRGCNS.PAR

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more