[English] 日本語
Yorodumi
- PDB-6j10: Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j10
TitleCiclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Hepatitis B virus / Ciclopirox / Capsid assembly inhibitor
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
6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype D subtype adw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, S. / Jin, M.S. / Cho, Y. / Kang, J. / Kim, S. / Park, M. / Park, H. / Kim, J. / Park, S. / Hwang, J. ...Park, S. / Jin, M.S. / Cho, Y. / Kang, J. / Kim, S. / Park, M. / Park, H. / Kim, J. / Park, S. / Hwang, J. / Kim, Y. / Kim, Y.J.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A6A3A11035008 Korea, Republic Of
National Research Foundation (Korea)NRF-2016R1A5A1007318 Korea, Republic Of
National Research Foundation (Korea)NRF-2017R1E1A1A01074299 Korea, Republic Of
National Research Foundation (Korea)NRF-2015M2A2A4A03044653 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly.
Authors: Kang, J.A. / Kim, S. / Park, M. / Park, H.J. / Kim, J.H. / Park, S. / Hwang, J.R. / Kim, Y.C. / Jun Kim, Y. / Cho, Y. / Sun Jin, M. / Park, S.G.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,7749
Polymers100,1526
Non-polymers6223
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-144 kcal/mol
Surface area38050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.924, 88.510, 99.162
Angle α, β, γ (deg.)90.00, 121.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-228-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 141
2010B1 - 141
1020A1 - 141
2020C1 - 141
1030A1 - 141
2030D1 - 141
1040A1 - 141
2040E1 - 141
1050A1 - 141
2050F1 - 141
1060B1 - 141
2060C1 - 141
1070B1 - 141
2070D1 - 141
1080B1 - 141
2080E1 - 141
1090B1 - 141
2090F1 - 141
10100C1 - 141
20100D1 - 141
10110C1 - 141
20110E1 - 141
10120C1 - 141
20120F1 - 141
10130D1 - 141
20130E1 - 141
10140D1 - 141
20140F1 - 141
10150E1 - 141
20150F1 - 141

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Capsid protein / Core protein


Mass: 16692.062 Da / Num. of mol.: 6 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus genotype D subtype adw
Production host: Escherichia coli (E. coli) / References: UniProt: P03147
#2: Chemical ChemComp-B4O / 6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one


Mass: 207.269 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H17NO2 / Comment: antifungal*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100mM ammonium citrate pH 6.0, 14% PEG5000MME, 2% hexylene glycol, 10% isopropanol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→84.89 Å / Num. obs: 47285 / % possible obs: 97.99 % / Redundancy: 3.5 % / Net I/σ(I): 30.1
Reflection shellResolution: 2.3→2.38 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30.7 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / SU B: 32.455 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30346 2382 4.8 %RANDOM
Rwork0.25747 ---
obs0.25975 47285 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.711 Å2
Baniso -1Baniso -2Baniso -3
1--3.44 Å20 Å21.59 Å2
2---4.66 Å2-0 Å2
3---3.57 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 45 292 6946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136864
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176266
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.6479424
X-RAY DIFFRACTIONr_angle_other_deg1.2521.57414450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.41821.056322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80315982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2011542
X-RAY DIFFRACTIONr_chiral_restr0.070.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021518
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.416.4693381
X-RAY DIFFRACTIONr_mcbond_other1.416.4713382
X-RAY DIFFRACTIONr_mcangle_it2.3999.6944215
X-RAY DIFFRACTIONr_mcangle_other2.3999.6934215
X-RAY DIFFRACTIONr_scbond_it1.2416.5733483
X-RAY DIFFRACTIONr_scbond_other1.2416.5743484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1269.8345210
X-RAY DIFFRACTIONr_long_range_B_refined6.97827768
X-RAY DIFFRACTIONr_long_range_B_other6.95427710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41790.11
12B41790.11
21A44180.08
22C44180.08
31A41540.12
32D41540.12
41A43670.09
42E43670.09
51A41460.11
52F41460.11
61B41990.12
62C41990.12
71B43710.08
72D43710.08
81B41800.12
82E41800.12
91B43310.08
92F43310.08
101C41850.13
102D41850.13
111C44800.07
112E44800.07
121C41950.11
122F41950.11
131D41720.12
132E41720.12
141D43400.09
142F43400.09
151E41930.11
152F41930.11
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 151 -
Rwork0.389 2979 -
obs--83.36 %
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)
11.9865-0.12790.42550.32520.1680.288-0.1187-0.0335-0.01770.01730.0398-0.0804-0.02220.03180.07890.05850.02320.02470.02140.04860.320223.5153-26.244619.6162
21.1712-0.12690.15921.20690.49870.2472-0.2638-0.14740.06560.10310.13060.212-0.00280.02820.13320.06620.04060.01350.0290.01270.33151.3408-16.289319.7119
30.91990.4793-0.01921.3386-0.45040.18820.0342-0.0735-0.0939-0.0223-0.05320.04750.02180.01080.0190.0277-0.01440.04410.0563-0.03850.31273.0237-71.798519.8749
41.52720.22540.23820.8245-0.22730.12550.088-0.25760.2053-0.0255-0.1921-0.14630.02930.00870.10420.0358-0.01650.00740.0767-0.01270.332622.5541-57.575319.6668
50.7238-0.5819-0.45041.72550.47070.3570.01270.0780.09640.0681-0.10040.0224-0.0131-0.07060.08770.0732-0.0123-0.05950.0181-0.02150.3227-26.3936-31.235719.7965
60.84570.0393-0.361.5545-0.17170.172-0.00190.106-0.20590.2953-0.1254-0.0738-0.0263-0.02910.12720.0885-0.0155-0.00360.02970.00380.3322-23.9136-55.230319.6903
70.0090.0083-0.01260.0109-0.0140.02060.0027-0.0109-0.0111-0.001-0.0080.00970.0046-0.00740.00530.47040.002-0.00020.4357-0.00150.43181.0716-41.775718.5942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 141
2X-RAY DIFFRACTION2B1 - 141
3X-RAY DIFFRACTION2B801
4X-RAY DIFFRACTION3C1 - 141
5X-RAY DIFFRACTION4D1 - 141
6X-RAY DIFFRACTION4D801
7X-RAY DIFFRACTION5E1 - 141
8X-RAY DIFFRACTION6F1 - 141
9X-RAY DIFFRACTION6F801
10X-RAY DIFFRACTION7A201 - 253
11X-RAY DIFFRACTION7B901 - 954
12X-RAY DIFFRACTION7C201 - 252
13X-RAY DIFFRACTION7D901 - 945
14X-RAY DIFFRACTION7E201 - 248
15X-RAY DIFFRACTION7F901 - 940

+
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://pdbjlvh1.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