[English] 日本語
Yorodumi
- PDB-9jqk: Ebola VP30 and its inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jqk
TitleEbola VP30 and its inhibitor
ComponentsTranscriptional activator VP30
KeywordsVIRAL PROTEIN / VP30
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / RNA binding / zinc ion binding / identical protein binding
Similarity search - Function
Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30
Similarity search - Domain/homology
: / Transcriptional activator VP30
Similarity search - Component
Biological speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsWu, F. / Xu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173865 China
CitationJournal: Antiviral Res. / Year: 2025
Title: Ginkgolic acid inhibits Ebola virus transcription and replication by disrupting the interaction between nucleoprotein and VP30 protein.
Authors: Peng, C. / Wu, F. / Ma, Y. / Liu, G. / Huang, Y. / Tong, R. / Xu, W.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Transcriptional activator VP30
A: Transcriptional activator VP30
B: Transcriptional activator VP30
C: Transcriptional activator VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0429
Polymers73,1874
Non-polymers8555
Water2,684149
1
D: Transcriptional activator VP30
A: Transcriptional activator VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4497
Polymers36,5932
Non-polymers8555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-52 kcal/mol
Surface area13100 Å2
MethodPISA
2
C: Transcriptional activator VP30

B: Transcriptional activator VP30


Theoretical massNumber of molelcules
Total (without water)36,5932
Polymers36,5932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3610 Å2
ΔGint-43 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.177, 54.042, 83.265
Angle α, β, γ (deg.)72.880, 85.961, 71.779
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Transcriptional activator VP30 / EbolaVP30 / eVP30 / Minor nucleoprotein VP30


Mass: 18296.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Strain: Kikwit-95 / Gene: VP30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q77DJ5
#2: Chemical ChemComp-A1ECX / 2-[(~{E})-heptadec-10-enyl]-6-oxidanyl-benzoic acid


Mass: 374.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H38O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350 and 200 mM ammonium phosphate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.29→79.55 Å / Num. obs: 31319 / % possible obs: 95.2 % / Redundancy: 1.7 % / CC1/2: 0.546 / Rmerge(I) obs: 0.099 / Net I/σ(I): 2.4
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 3107 / CC1/2: 0.547 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→48.52 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.425 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.236
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 1546 4.936 %RANDOM
Rwork0.2184 29773 --
all0.221 ---
obs-29773 95.14 %-
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: 45.408 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å20.007 Å2-0.005 Å2
2--0.014 Å2-0.002 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 2.29→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 57 149 4246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124162
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164160
X-RAY DIFFRACTIONr_angle_refined_deg0.621.8395618
X-RAY DIFFRACTIONr_angle_other_deg0.2471.7559556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5965504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.0765.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86810772
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.79410172
X-RAY DIFFRACTIONr_chiral_restr0.0330.2664
X-RAY DIFFRACTIONr_chiral_restr_other0.1910.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024830
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02954
X-RAY DIFFRACTIONr_nbd_refined0.2011926
X-RAY DIFFRACTIONr_symmetry_nbd_other0.18613579
X-RAY DIFFRACTIONr_nbtor_refined0.16712069
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.06711960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1411164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.02911
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.176110
X-RAY DIFFRACTIONr_nbd_other0.154179
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.11815
X-RAY DIFFRACTIONr_mcbond_it4.0834.2452028
X-RAY DIFFRACTIONr_mcbond_other4.0734.2452028
X-RAY DIFFRACTIONr_mcangle_it5.6677.6542528
X-RAY DIFFRACTIONr_mcangle_other5.6667.6542529
X-RAY DIFFRACTIONr_scbond_it5.9845.0062134
X-RAY DIFFRACTIONr_scbond_other5.9825.0082135
X-RAY DIFFRACTIONr_scangle_it8.9828.8923090
X-RAY DIFFRACTIONr_scangle_other8.9818.8933091
X-RAY DIFFRACTIONr_lrange_it10.68452.5216838
X-RAY DIFFRACTIONr_lrange_other10.68552.49116777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.3490.341020.3332244X-RAY DIFFRACTION95.3271
2.349-2.4140.3611110.3282149X-RAY DIFFRACTION95.7627
2.414-2.4830.341230.3022105X-RAY DIFFRACTION96.8696
2.483-2.560.2951250.2722090X-RAY DIFFRACTION97.7062
2.56-2.6430.2791080.2421960X-RAY DIFFRACTION97.824
2.643-2.7360.26830.2371999X-RAY DIFFRACTION97.7465
2.736-2.8390.3131000.231880X-RAY DIFFRACTION97.8744
2.839-2.9540.282880.2251813X-RAY DIFFRACTION97.8888
2.954-3.0850.27640.2081784X-RAY DIFFRACTION98.2456
3.085-3.2350.236800.211660X-RAY DIFFRACTION98.6395
3.235-3.4090.3800.1961584X-RAY DIFFRACTION97.9976
3.409-3.6150.208700.1921300X-RAY DIFFRACTION84.5157
3.615-3.8630.252560.1961081X-RAY DIFFRACTION74.6553
3.863-4.170.232540.1861053X-RAY DIFFRACTION78.678
4.17-4.5650.268750.1841188X-RAY DIFFRACTION98.749
4.565-5.0980.198690.1621090X-RAY DIFFRACTION99.2295
5.098-5.8760.259540.209976X-RAY DIFFRACTION98.9433
5.876-7.170.243530.238801X-RAY DIFFRACTION99.3023
7.17-10.0310.2260.182655X-RAY DIFFRACTION99.4161
10.031-48.520.375250.326355X-RAY DIFFRACTION97.9381

+
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