[English] 日本語
Yorodumi
- PDB-9n3h: Crystal structure of HBV capsid with compound 18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n3h
TitleCrystal structure of HBV capsid with compound 18
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / HBV capsid
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 core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus genotype D subtype adw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.543 Å
AuthorsWhite, A. / Lakshminarasimhan, D. / Cakici, O. / Suto, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of VNRX-9945, a Potent, Broadly Active Capsid Assembly Modulator as a Clinical Candidate for the Treatment of Chronic Hepatitis B Virus Infection.
Authors: Liu, B. / Yao, J. / Haimowitz, T. / Benetatos, C.A. / Boyd, S.A. / Condon, S.M. / Burns, C.J. / White, A. / Lakshminarasimhan, D. / Suto, R.K. / Cakici, O. / Drager, A.S. / Hart, S.G.E. / ...Authors: Liu, B. / Yao, J. / Haimowitz, T. / Benetatos, C.A. / Boyd, S.A. / Condon, S.M. / Burns, C.J. / White, A. / Lakshminarasimhan, D. / Suto, R.K. / Cakici, O. / Drager, A.S. / Hart, S.G.E. / Pevear, D.C. / Coburn, G.A.
History
DepositionJan 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9044
Polymers36,0092
Non-polymers8952
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-32 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.152, 88.152, 290.557
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

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


Mass: 18004.578 Da / Num. of mol.: 2 / Mutation: Y132A
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03147
#2: Chemical ChemComp-A1BVU / N-[3-(difluoromethyl)phenyl]-5-[{[(1s,4s)-4-hydroxycyclohexyl]amino}(oxo)acetyl]-1,2,4-trimethyl-1H-pyrrole-3-carboxamide


Mass: 447.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27F2N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13-18% (v/v) MPD, 280-310 mM trisodium citrate, and 100 mM Hepes pH 7.5. Protein:reservoir ratio of 2:1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.54→48.473 Å / Num. obs: 14719 / % possible obs: 99.8 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.044 / Rrim(I) all: 0.132 / Χ2: 0.92 / Net I/σ(I): 8.2
Reflection shellResolution: 2.54→2.66 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1753 / CC1/2: 0.924 / Rpim(I) all: 0.336 / Rrim(I) all: 0.982 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.543→48.473 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: FREE R-VALUE / ESU R: 0.438 / ESU R Free: 0.305
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2966 779 5.292 %
Rwork0.2605 13940 -
all0.262 --
obs-14719 99.79 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 88.676 Å2
Baniso -1Baniso -2Baniso -3
1--8.776 Å2-4.388 Å20 Å2
2---8.776 Å20 Å2
3---28.47 Å2
Refinement stepCycle: LAST / Resolution: 2.543→48.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 64 6 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162071
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.8413089
X-RAY DIFFRACTIONr_angle_other_deg0.7991.754764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0665264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.008513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02710322
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.6651091
X-RAY DIFFRACTIONr_chiral_restr0.0590.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022601
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02515
X-RAY DIFFRACTIONr_nbd_refined0.2510.2588
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.21865
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21106
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1540.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.26
X-RAY DIFFRACTIONr_nbd_other0.210.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.22
X-RAY DIFFRACTIONr_mcbond_it6.598.9271068
X-RAY DIFFRACTIONr_mcbond_other6.5848.9281068
X-RAY DIFFRACTIONr_mcangle_it10.56816.0011328
X-RAY DIFFRACTIONr_mcangle_other10.56816.0011329
X-RAY DIFFRACTIONr_scbond_it6.1239.1441183
X-RAY DIFFRACTIONr_scbond_other6.1219.1471184
X-RAY DIFFRACTIONr_scangle_it10.19616.7871761
X-RAY DIFFRACTIONr_scangle_other10.19316.7881762
X-RAY DIFFRACTIONr_lrange_it15.0486.1172643
X-RAY DIFFRACTIONr_lrange_other15.05186.0832641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.543-2.6090.501580.4399920.44310610.2340.37998.96320.373
2.609-2.680.487640.5159870.51310520.4070.35299.90490.457
2.68-2.7580.419430.4769700.47310130.4970.3431000.412
2.758-2.8420.458430.4349380.4359830.4820.38199.79650.382
2.842-2.9350.383590.4148960.4129560.3130.43399.89540.356
2.935-3.0380.34510.4198840.4159350.5270.4721000.375
3.038-3.1520.398420.4028410.4028880.5170.49999.43690.367
3.152-3.280.429450.3618140.3648600.5150.55599.88370.338
3.28-3.4250.276420.3227870.328300.7820.70199.87950.3
3.425-3.5920.283470.2837450.2837920.9270.8431000.268
3.592-3.7850.201390.2247290.2237680.9680.9461000.22
3.785-4.0130.266370.1856910.1897280.9580.9691000.182
4.013-4.2880.221340.1546310.1576650.9530.9791000.154
4.288-4.6280.188280.1466210.1486500.9830.98299.84620.151
4.628-5.0650.22380.1685450.1725840.9690.97799.82880.181
5.065-5.6560.304300.1915060.1975360.9460.9751000.201
5.656-6.5160.334230.2284590.2334820.9490.9671000.243
6.516-7.9440.328200.2143960.224160.9360.9671000.23
7.944-11.0870.205240.1823100.1843370.9780.97799.10980.217
11.087-48.4730.445120.2481980.2582100.8190.9591000.291

+
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