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- PDB-5d7y: Crystal structure of Hepatitis B virus T=4 capsid in complex with... -

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Basic information

Entry
Database: PDB / ID: 5d7y
TitleCrystal structure of Hepatitis B virus T=4 capsid in complex with the allosteric modulator HAP18
ComponentsCapsid protein
KeywordsVIRUS/INHIBITOR / capsid / core protein / hepadnavirus / icosahedral / assembly effector / assembly accelerator / allosteric modulator / HAP / VIRUS-INHIBITOR complex
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
Chem-58H / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype D subtype adw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.894 Å
AuthorsVenkatakrishnan, B. / Katen, S.P. / Zlotnick, A.
CitationJournal: J.Virol. / Year: 2016
Title: Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket.
Authors: Venkatakrishnan, B. / Katen, S.P. / Francis, S. / Chirapu, S. / Finn, M.G. / Zlotnick, A.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.journal_id_CSD
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3356
Polymers67,2934
Non-polymers1,0422
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,100,078360
Polymers4,037,560240
Non-polymers62,518120
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: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 342 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)341,67330
Polymers336,46320
Non-polymers5,21010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 410 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)410,00836
Polymers403,75624
Non-polymers6,25212
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: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.1 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,100,078360
Polymers4,037,560240
Non-polymers62,518120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)529.375, 367.411, 542.002
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5618, 0.4229, 0.711), (-0.8101, 0.4557, 0.369), (-0.1679, -0.7833, 0.5986)-50.5602, 30.3973, 69.0632
3generate(-0.1469, -0.1253, 0.9812), (-0.887, -0.4224, -0.1867), (0.4378, -0.8977, -0.0491)-16.8126, 110.9406, 94.9327
4generate(-0.1482, -0.8875, 0.4362), (-0.1261, -0.4205, -0.8985), (0.9809, -0.1882, -0.0496)55.0199, 130.3288, 41.9527
5generate(0.5598, -0.8114, -0.1683), (0.4278, 0.4568, -0.7799), (0.7097, 0.3646, 0.6028)65.0306, 59.78, -17.42
6generate(-0.1215, 0.0959, 0.9879), (0.0971, -0.9894, 0.108), (0.9878, 0.1091, 0.1109)-20.1541, -24.2493, 19.9722
7generate(-0.3105, 0.8383, 0.4481), (-0.7802, -0.4941, 0.3837), (0.543, -0.2305, 0.8075)69.2806, 25.2356, -28.0416
8generate(0.4936, -0.3761, 0.7842), (0.8014, 0.547, -0.2421), (-0.3379, 0.7479, 0.5714)-54.139, -47.4541, 89.7577
9generate(-0.3164, -0.7798, 0.5403), (0.8373, -0.4972, -0.2273), (0.4458, 0.3805, 0.8102)57.8091, -52.8783, -18.8885
10generate(-0.9306, -0.1019, 0.3515), (-0.1012, -0.8513, -0.5148), (0.3517, -0.5147, 0.7819)143.0774, 78.1774, -5.575
11generate(0.4561, -0.5715, 0.6822), (0.0491, 0.7816, 0.6219), (-0.8886, -0.2502, 0.3845)-35.8558, -86.5636, 167.6915
12generate(0.3615, -0.915, -0.1791), (0.9109, 0.3056, 0.2773), (-0.199, -0.2634, 0.9439)85.0478, -126.2879, 27.5205
13generate(0.9758, -0.1136, -0.1867), (0.2134, 0.3116, 0.9259), (-0.047, -0.9434, 0.3283)27.2342, -142.5307, 92.5692
14generate(0.3835, -0.1587, -0.9098), (0.549, 0.8314, 0.0864), (0.7427, -0.5326, 0.4059)179.6242, -64.9701, 5.739
15generate(0.7351, -0.4303, 0.524), (-0.4309, -0.8931, -0.1289), (0.5234, -0.131, -0.8419)-42.1856, 59.2825, 190.0783
16generate(0.6794, 0.4994, 0.5375), (-0.2891, -0.4911, 0.8217), (0.6744, -0.7137, -0.1893)-40.1359, -79.7333, 90.8159
17generate(0.4958, 0.8016, -0.334), (-0.3769, 0.5451, 0.7489), (0.7824, -0.2454, 0.5724)93.4373, -61.6361, -20.7433
18generate(0.674, -0.2893, 0.6797), (0.506, -0.4897, -0.7101), (0.5383, 0.8225, -0.1837)-57.6149, 43.443, 102.7885
19generate(0.455, 0.0511, -0.889), (-0.5723, 0.7816, -0.2479), (0.6822, 0.6216, 0.3849)169.7069, 88.5546, 14.3044
20generate(0.5643, 0.681, 0.4667), (0.6825, -0.7029, 0.2002), (0.4644, 0.2056, -0.8614)-18.4543, -93.3955, 198.5856
21generate(-0.3092, 0.9193, 0.2435), (0.1892, -0.1915, 0.9631), (0.932, 0.3438, -0.1147)95.5732, -145.0616, 55.4829
22generate(0.9759, 0.2132, -0.0469), (-0.1146, 0.318, -0.9411), (-0.1857, 0.9238, 0.3347)8.2003, 133.9511, 105.4657
23generate(0.3669, 0.9099, -0.1938), (-0.9117, 0.3103, -0.2692), (-0.1848, 0.2754, 0.9434)87.5576, 124.5319, 25.437
24generate(-0.3168, 0.1838, 0.9305), (0.9178, -0.1883, 0.3496), (0.2395, 0.9648, -0.109)7.3097, -136.2482, 121.6378
25generate(-0.959, 0.1043, 0.2636), (0.0954, -0.757, 0.6464), (0.2669, 0.6451, 0.716)156.1863, -94.992, 11.8365
26generate(0.386, 0.5485, 0.7417), (-0.1599, 0.8317, -0.5317), (-0.9085, 0.0867, 0.4088)-37.0133, 84.9737, 166.3178
27generate(-0.4981, 0.7204, 0.4826), (-0.7198, -0.0333, -0.6934), (-0.4835, -0.6927, 0.5351)82.8121, 160.7393, 108.6286
28generate(-0.5015, -0.7154, -0.4865), (0.7237, -0.0387, -0.6891), (0.4741, -0.6977, 0.5371)210.9211, 18.9048, 14.1546
29generate(0.603, -0.6033, 0.5219), (-0.7113, -0.1104, 0.6942), (-0.3612, -0.7898, -0.4957)-29.6755, -21.8306, 231.6497
30generate(0.6043, -0.7099, -0.3618), (-0.6001, -0.1068, -0.7927), (0.5241, 0.6961, -0.4906)85.8537, 162.035, 144.2058
31generate(-0.4839, 0.6122, -0.6253), (-0.775, 0.032, 0.6311), (0.4064, 0.7901, 0.4589)226.9403, -7.3621, 31.2101
32generate(0.3804, 0.7109, 0.5915), (0.7632, 0.12, -0.635), (-0.5224, 0.693, -0.4969)-17.5585, 7.504, 247.7742
33generate(-0.9971, 0.0616, 0.0448), (0.0647, 0.3745, 0.925), (0.0402, 0.9252, -0.3774)190.284, -127.4383, 176.5669
34generate(0.2905, 0.1842, -0.939), (-0.8768, -0.3417, -0.3383), (-0.3832, 0.9216, 0.0623)192.6875, 129.5212, 160.2601
35generate(0.9372, 0.226, -0.2656), (0.022, -0.7983, -0.6019), (-0.3481, 0.5583, -0.7531)41.1673, 76.7128, 264.0152
36generate(-0.4252, -0.488, -0.7623), (-0.877, 0.4305, 0.2136), (0.2239, 0.7593, -0.611)238.6207, 56.8254, 189.7265
37generate(-0.5031, 0.8513, 0.1491), (0.8527, 0.4609, 0.2457), (0.1405, 0.2507, -0.9578)127.9015, -116.5489, 242.5165
38generate(-0.4621, 0.4459, -0.7666), (0.0297, 0.8717, 0.4891), (0.8863, 0.2032, -0.416)244.0493, -67.2768, 98.682
39generate(-0.3565, -0.6735, -0.6475), (-0.1651, 0.7276, -0.6659), (0.9196, -0.1304, -0.3706)217.5714, 102.7768, 89.824
40generate(0.3831, 0.7638, -0.5194), (0.7133, 0.1126, 0.6917), (0.5868, -0.6355, -0.5017)128.2908, -161.2467, 139.4057
41generate(-0.9471, -0.2542, 0.1961), (-0.2551, 0.2249, -0.9404), (0.1949, -0.9406, -0.2778)165.0689, 148.2459, 148.59
42generate(0.1702, -0.1513, -0.9737), (0.9402, -0.271, 0.2065), (-0.2951, -0.9506, 0.0961)208.9914, -119.5912, 147.593
43generate(-0.6162, 0.2914, -0.7317), (0.733, 0.552, -0.3974), (0.2881, -0.7813, -0.5538)253.8497, -20.5913, 175.8507
44generate(0.9355, 0.0234, -0.3526), (0.2293, -0.7995, 0.5552), (-0.269, -0.6002, -0.7533)52.0809, -95.2189, 256.6542
45generate(-0.2206, -0.9468, 0.2342), (-0.9464, 0.1497, -0.2863), (0.236, -0.2848, -0.9291)88.5207, 130.1689, 230.2781
46generate(-0.4272, -0.8774, 0.2183), (-0.4931, 0.4284, 0.7572), (-0.7579, 0.2158, -0.6156)111.9221, -51.1355, 285.8802
47generate(-0.6183, 0.7298, 0.2916), (0.2908, 0.5572, -0.7778), (-0.7301, -0.3962, -0.5567)119.8735, 72.8217, 276.0987
48generate(0.1097, 0.0636, -0.9919), (0.0545, -0.9968, -0.0579), (-0.9925, -0.0477, -0.1129)216.6985, 1.5276, 243.3374
49generate(0.1824, 0.851, -0.4924), (0.8477, -0.3899, -0.3598), (-0.4982, -0.3517, -0.7925)144.3237, -36.68, 283.7294
50generate(0.434, -0.7509, -0.4978), (-0.7529, -0.6058, 0.2573), (-0.4948, 0.2631, -0.8282)120.7226, 39.5648, 288.0778
51generate(-0.9878, -0.1559, 0.0036), (-0.1559, 0.9861, -0.0576), (0.0054, -0.0575, -0.9983)194.1253, 21.885, 261.3914
52generate(0.1699, 0.9411, -0.2924), (-0.1513, -0.2683, -0.9514), (-0.9738, 0.2059, 0.0968)119.4274, 139.7738, 214.4747
53generate(-0.6218, -0.4194, -0.6614), (-0.4279, -0.5254, 0.7354), (-0.6559, 0.7403, 0.1472)244.7832, -54.4879, 176.975
54generate(-0.4629, 0.0274, 0.886), (0.4445, 0.872, 0.2052), (-0.7669, 0.4888, -0.4158)26.617, -70.693, 261.3437
55generate(-0.4905, -0.7741, 0.4002), (0.6059, 0.0271, 0.795), (-0.6263, 0.6325, 0.4558)93.2468, -164.426, 132.7437
56generate(-0.6577, 0.5613, -0.5024), (-0.5669, -0.808, -0.1607), (-0.4962, 0.1791, 0.8495)228.9153, 76.3928, 67.9547
57generate(-0.7408, 0.3644, -0.5643), (0.3673, -0.4837, -0.7944), (-0.5625, -0.7958, 0.2245)244.4662, 68.3411, 157.4399
58generate(0.2805, -0.8774, -0.3891), (0.183, -0.3491, 0.9191), (-0.9422, -0.329, 0.0626)120.9694, -138.7172, 216.058
59generate(-0.3604, -0.1689, 0.9174), (-0.6697, 0.7314, -0.1285), (-0.6493, -0.6607, -0.3768)12.3573, 82.5276, 244.8252
60generate(-0.6584, -0.5643, -0.4981), (0.5599, -0.8094, 0.177), (-0.5031, -0.1624, 0.8489)228.4808, -78.3131, 68.7481

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Components

#1: Protein
Capsid protein / Core antigen / Core protein / HBcAg / p21.5


Mass: 16823.168 Da / Num. of mol.: 4 / Fragment: UNP residues 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)
Strain: isolate United Kingdom/adyw/1979 / Gene: C / Variant: Cp150 / Plasmid: pET11C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03147
#2: Chemical ChemComp-58H / methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate


Mass: 520.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26ClFN4O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.31 Å3/Da / Density % sol: 80.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 5% PEG5000 MME, 5% PEG8000, 14% 2,3-butanediol, 100 mM Tris, pH 9.0, 150 mM sodium chloride, 300 mM potassium chloride

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.894→35.682 Å / Num. all: 1368744 / Num. obs: 826742 / % possible obs: 93.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.71
Reflection shellResolution: 3.89→3.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.48 / % possible all: 77.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QGT

1qgt


Resolution: 3.894→35.682 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 1964 0.24 %
Rwork0.2626 --
obs0.2626 810969 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.894→35.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 74 0 4610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004285360
X-RAY DIFFRACTIONf_angle_d0.964391440
X-RAY DIFFRACTIONf_dihedral_angle_d17.893103320
X-RAY DIFFRACTIONf_chiral_restr0.0743920
X-RAY DIFFRACTIONf_plane_restr0.00649200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8935-3.99080.4053890.426437609X-RAY DIFFRACTION58
3.9908-4.09850.43911270.41451670X-RAY DIFFRACTION80
4.0985-4.2190.39561270.401752274X-RAY DIFFRACTION81
4.219-4.35490.39531280.390152748X-RAY DIFFRACTION81
4.3549-4.51030.39511310.374453433X-RAY DIFFRACTION83
4.5103-4.69050.37751340.349355282X-RAY DIFFRACTION85
4.6905-4.90340.32721400.322457789X-RAY DIFFRACTION89
4.9034-5.16120.31621500.299161867X-RAY DIFFRACTION96
5.1612-5.48350.28851560.299464206X-RAY DIFFRACTION99
5.4835-5.90510.35091560.289564484X-RAY DIFFRACTION99
5.9051-6.49620.26151570.273664596X-RAY DIFFRACTION100
6.4962-7.42880.28541570.248864836X-RAY DIFFRACTION100
7.4288-9.33170.19641580.195664904X-RAY DIFFRACTION100
9.3317-35.68380.19931540.188663307X-RAY DIFFRACTION97

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