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- PDB-5wre: Hepatitis B virus core protein Y132A mutant in complex with heter... -

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Basic information

Entry
Database: PDB / ID: 5wre
TitleHepatitis B virus core protein Y132A mutant in complex with heteroaryldihydropyrimidine (HAP_R01)
ComponentsCore protein
KeywordsVIRAL PROTEIN / HEPATITIS B VIRUS / HBV / CORE PROTEIN / CAPSID / Y132A DIMER / Y132A HEXAMER / heteroaryldihydropyrimidine / HAP
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
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-7TL / ISOPROPYL ALCOHOL / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.946 Å
AuthorsZhou, Z. / Xu, Z.H.
CitationJournal: Sci Rep / Year: 2017
Title: Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms.
Authors: Zhou, Z. / Hu, T. / Zhou, X. / Wildum, S. / Garcia-Alcalde, F. / Xu, Z. / Wu, D. / Mao, Y. / Tian, X. / Zhou, Y. / Shen, F. / Zhang, Z. / Tang, G. / Najera, I. / Yang, G. / Shen, H.C. / Young, J.A. / Qin, N.
History
DepositionDec 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein
B: Core protein
C: Core protein
D: Core protein
E: Core protein
F: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,09128
Polymers104,9216
Non-polymers4,16922
Water9,080504
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-115 kcal/mol
Surface area39590 Å2
Unit cell
Length a, b, c (Å)65.241, 66.930, 87.071
Angle α, β, γ (deg.)68.280, 69.020, 83.620
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1 or (resid 2 and (name...
21(chain B and (resseq 1 or (resid 2 and (name...
31(chain C and (resseq 1 or (resid 2 and (name...
41(chain D and (resseq 1 or (resid 2 and (name...
51(chain E and (resseq 1 or (resid 2 and (name...
61(chain F and (resseq 1 or (resid 2 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and (resseq 1 or (resid 2 and (name...AA11
12ASPASPASPASP(chain A and (resseq 1 or (resid 2 and (name...AA22
13METMETTHRTHR(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1421 - 142
14METMETTHRTHR(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1421 - 142
15METMETTHRTHR(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1421 - 142
16METMETTHRTHR(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1421 - 142
17METMETTHRTHR(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1421 - 142
18METMETTHRTHR(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1421 - 142
21METMETMETMET(chain B and (resseq 1 or (resid 2 and (name...BB11
22ASPASPASPASP(chain B and (resseq 1 or (resid 2 and (name...BB22
23METMETTHRTHR(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1421 - 142
24METMETTHRTHR(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1421 - 142
25METMETTHRTHR(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1421 - 142
26METMETTHRTHR(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1421 - 142
27METMETTHRTHR(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1421 - 142
28METMETTHRTHR(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1421 - 142
31METMETMETMET(chain C and (resseq 1 or (resid 2 and (name...CC11
32ASPASPASPASP(chain C and (resseq 1 or (resid 2 and (name...CC22
33METMETTHRTHR(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1421 - 142
34METMETTHRTHR(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1421 - 142
35METMETTHRTHR(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1421 - 142
36METMETTHRTHR(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1421 - 142
37METMETTHRTHR(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1421 - 142
38METMETTHRTHR(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1421 - 142
41METMETMETMET(chain D and (resseq 1 or (resid 2 and (name...DD11
42ASPASPASPASP(chain D and (resseq 1 or (resid 2 and (name...DD22
43METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
44METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
45METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
46METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
47METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
48METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
51METMETMETMET(chain E and (resseq 1 or (resid 2 and (name...EE11
52ASPASPASPASP(chain E and (resseq 1 or (resid 2 and (name...EE22
53METMETTHRTHR(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1421 - 142
54METMETTHRTHR(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1421 - 142
55METMETTHRTHR(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1421 - 142
56METMETTHRTHR(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1421 - 142
57METMETTHRTHR(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1421 - 142
58METMETTHRTHR(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1421 - 142
61METMETMETMET(chain F and (resseq 1 or (resid 2 and (name...FF11
62ASPASPASPASP(chain F and (resseq 1 or (resid 2 and (name...FF22
63METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
64METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
65METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
66METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
67METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
68METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Core protein


Mass: 17486.916 Da / Num. of mol.: 6 / Fragment: UNP residues 1-149 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: L7R9I1

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Non-polymers , 5 types, 526 molecules

#2: Chemical
ChemComp-7TL / (2S)-1-[[(4R)-4-(2-chloranyl-4-fluoranyl-phenyl)-5-methoxycarbonyl-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-4,4-bis(fluoranyl)pyrrolidine-2-carboxylic acid


Mass: 514.905 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H18ClF3N4O4S
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM citrate, 21%(vol/vol) isopropanol, 1%(W/V) PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.946→50 Å / Num. obs: 90050 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.95 Å2 / Rmerge(I) obs: 0.1 / Net I/av σ(I): 13.525 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.95-1.983.80.7620.768195.8
1.98-2.023.90.6180.832196.4
2.02-2.0640.5520.849196.2
2.06-2.140.4840.941196.4
2.1-2.1540.3870.929196.5
2.15-2.24.10.3490.941196.8
2.2-2.254.10.3280.951196.6
2.25-2.314.10.2540.961196.8
2.31-2.384.10.2320.963197.2
2.38-2.464.10.2130.965197.4
2.46-2.544.10.1990.973197.4
2.54-2.654.10.1730.978197.4
2.65-2.774.10.1430.979197.4
2.77-2.914.10.1270.983197.7
2.91-3.14.10.110.981198
3.1-3.334.10.0880.99197.9
3.33-3.674.10.0770.99197.6
3.67-4.24.10.0630.991197
4.2-5.294.10.0540.994197.3
5.29-504.20.0480.997198.9

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMG

4bmg


Resolution: 1.946→33.204 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.79
RfactorNum. reflection% reflection
Rfree0.2388 2196 2.44 %
Rwork0.2068 --
obs0.2076 89929 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.22 Å2 / Biso mean: 41.7471 Å2 / Biso min: 16.54 Å2
Refinement stepCycle: final / Resolution: 1.946→33.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 271 504 7663
Biso mean--35.7 50.74 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097461
X-RAY DIFFRACTIONf_angle_d0.94410253
X-RAY DIFFRACTIONf_chiral_restr0.0551138
X-RAY DIFFRACTIONf_plane_restr0.0071293
X-RAY DIFFRACTIONf_dihedral_angle_d18.3094309
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3275X-RAY DIFFRACTION10.426TORSIONAL
12B3275X-RAY DIFFRACTION10.426TORSIONAL
13C3275X-RAY DIFFRACTION10.426TORSIONAL
14D3275X-RAY DIFFRACTION10.426TORSIONAL
15E3275X-RAY DIFFRACTION10.426TORSIONAL
16F3275X-RAY DIFFRACTION10.426TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9457-1.9880.37031090.32254471458079
1.988-2.03430.34761370.2915550568796
2.0343-2.08510.32821340.26955477561196
2.0851-2.14150.28871310.24165525565696
2.1415-2.20450.26261360.22845540567696
2.2045-2.27570.25661520.21885454560697
2.2757-2.3570.2251340.19275562569697
2.357-2.45130.25061430.19545546568997
2.4513-2.56280.26921380.20675566570498
2.5628-2.69790.23361420.20325546568897
2.6979-2.86680.24141390.19555573571297
2.8668-3.0880.23041440.20085568571298
3.088-3.39850.21581400.1895606574698
3.3985-3.88970.2311370.18575577571498
3.8897-4.8980.17921370.18285516565397
4.898-33.20890.25691430.22485656579999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2737-1.4118-0.85981.85260.17943.3084-0.0601-0.0832-0.01170.10840.0562-0.0817-0.2205-0.0356-0.01090.2517-0.0555-0.04570.2253-0.04070.2195-38.96122.78219.7866
21.1514-0.35670.6552.1510.80982.7048-0.0099-0.0105-0.17850.1673-0.01850.51730.2988-0.4130.0580.2197-0.04960.04710.2908-0.02220.3068-47.3773-3.454415.3976
31.8994-0.2194-1.59121.8642-1.43045.6087-0.1953-0.23090.09740.16510.28770.0926-0.2597-0.294-0.07340.33690.0809-0.01460.3689-0.00160.2585-39.94113.505938.1509
41.9051-1.3505-0.22362.26870.45322.81720.0460.00840.0391-0.1145-0.0460.0076-0.0777-0.0161-0.03240.1746-0.08860.02460.25120.03980.2353-32.0786-3.0281.9436
51.6551-0.3056-0.66431.4746-0.79831.9659-0.05330.2341-0.2012-0.0670.07680.25270.2225-0.353-0.01410.2363-0.0750.01560.2533-0.0470.2759-40.5708-10.2614.4229
62.8485-0.9231.08630.97710.10076.17190.4010.04930.0489-0.1391-0.3029-0.12760.40660.2932-0.03850.31150.01570.01960.20910.0340.2346-29.0775-1.9969-16.1209
72.1101-1.76930.73422.1134-0.35312.50690.09910.05080.113-0.1709-0.1087-0.04480.08740.15010.00940.229-0.05680.00960.20160.04940.2853-9.9578-28.83082.4111
81.099-1.3151-0.94932.79-0.58773.0254-0.02330.1279-0.2532-0.1448-0.04320.55550.5941-0.43310.07260.3028-0.0775-0.04030.2641-0.01130.2584-16.0588-38.43662.658
93.6352-1.93051.26073.1501-1.26592.95510.15830.1868-0.3621-0.2465-0.125-0.0688-0.11080.10770.12680.2364-0.01190.01080.1704-0.00780.2007-18.2804-15.8297-7.3875
101.8866-1.5244-1.10412.4263-0.4163.6284-0.1827-0.15190.01130.01170.144-0.04870.31530.27990.05870.1642-0.0282-0.05280.29430.01610.2676-3.7195-39.940919.84
112.2679-0.83050.54930.59430.19432.5401-0.07520.0111-0.3191-0.02170.12880.22840.3409-0.2050.0210.2566-0.096-0.00920.23980.02330.3112-12.6981-40.867116.7107
121.8797-1.2310.48353.1786-1.45813.4001-0.0939-0.17310.10480.06260.1680.50570.12850.30010.11570.23360.05060.01640.31320.00050.2497.1134-48.557229.7028
130.94630.886-1.81417.055-2.24423.5477-0.1564-0.17110.3872-0.0340.06850.192-0.08920.45170.11880.4532-0.1855-0.17110.56830.14340.82666.8555-22.46614.3501
142.3789-2.0205-0.72023.7383-0.22712.50750.01540.03960.0346-0.1001-0.08140.03070.13810.07850.03080.23380.0225-0.00440.2627-0.01480.2672-17.0496-26.550348.0589
153.1899-0.733-0.21792.490.17852.9484-0.09890.1027-0.566-0.05770.15840.62230.4029-0.4166-0.10210.27880.0079-0.01580.25940.06090.3888-27.1091-31.671349.2954
161.8042-1.9263-0.52454.21072.14623.4101-0.1133-0.22320.05240.1778-0.0070.01480.39870.3358-0.05710.27270.07950.04520.31320.0240.2254-4.7284-37.440540.2814
173.1249-2.19090.39982.284-0.38772.2427-0.0782-0.19-0.11830.0550.12230.0724-0.0526-0.1656-0.04550.30620.01730.01260.2309-0.00640.2731-32.0738-11.328150.4892
182.0948-1.64760.48483.38020.34173.62350.27290.0516-0.5262-0.2124-0.1580.53940.3377-0.4859-0.08190.30640.0377-0.04340.30930.00310.3804-34.383-19.674446.1164
193.543-1.2061-0.91861.4096-0.1332.16370.04770.33950.2187-0.0224-0.0833-0.2267-0.3798-0.3016-0.00560.32360.0523-0.01090.2603-0.02010.2588-40.3981.54157.5755
203.18791.85011.90442.37480.96151.1896-0.2037-0.39320.48630.4658-0.13240.1744-0.2861-0.08790.07310.834-0.0373-0.05810.6188-0.02270.9968-22.239326.377555.1419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 49 )A1 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 110 )A50 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 142 )A111 - 142
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 49 )B1 - 49
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 110 )B50 - 110
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 142 )B111 - 142
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 49 )C1 - 49
8X-RAY DIFFRACTION8chain 'C' and (resid 50 through 110 )C50 - 110
9X-RAY DIFFRACTION9chain 'C' and (resid 111 through 142 )C111 - 142
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 42 )D1 - 42
11X-RAY DIFFRACTION11chain 'D' and (resid 43 through 110 )D43 - 110
12X-RAY DIFFRACTION12chain 'D' and (resid 111 through 144 )D111 - 144
13X-RAY DIFFRACTION13chain 'D' and (resid 150 through 155 )D150 - 155
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 49 )E1 - 49
15X-RAY DIFFRACTION15chain 'E' and (resid 50 through 110 )E50 - 110
16X-RAY DIFFRACTION16chain 'E' and (resid 111 through 142 )E111 - 142
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 42 )F1 - 42
18X-RAY DIFFRACTION18chain 'F' and (resid 43 through 110 )F43 - 110
19X-RAY DIFFRACTION19chain 'F' and (resid 111 through 143 )F111 - 143
20X-RAY DIFFRACTION20chain 'F' and (resid 149 through 155)F149 - 155

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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

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