PDB-9jqk: Ebola VP30 and its inhibitor

ID or keywords:

Entry

Database: PDB / ID: 9jqk

Title

Ebola VP30 and its inhibitor

Components

Transcriptional activator VP30

Keywords

VIRAL 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

Biological species

Ebola virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Wu, F. / Xu, W.

Funding support

China, 1items

Citation

Journal: 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

Deposition	Sep 27, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jqk.cif.gz	121.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9jqk.ent.gz		Display	PDB format
PDBx/mmJSON format	9jqk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jqk_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9jqk_full_validation.pdf.gz	1 MB	Display
Data in XML	9jqk_validation.xml.gz	24.2 KB	Display
Data in CIF	9jqk_validation.cif.gz	31.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jq/9jqk ftp://data.pdbj.org/pub/pdb/validation_reports/jq/9jqk	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#178 - Oct 2014 Ebola Virus Proteins similarity (3)

Deposited unit

D: Transcriptional activator VP30

A: Transcriptional activator VP30

B: Transcriptional activator VP30

C: Transcriptional activator VP30

hetero molecules

74 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Transcriptional activator VP30

A: Transcriptional activator VP30

hetero molecules

defined by author&software
37.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Transcriptional activator VP30

B: Transcriptional activator VP30

defined by author&software
36.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1

#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 interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97915 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.29→79.55 Å / Num. obs: 31319 / % possible obs: 95.2 % / Redundancy: 1.7 % / CC_1/2: 0.546 / R_merge(I) obs: 0.099 / Net I/σ(I): 2.4
Reflection shell	Resolution: 2.29→2.37 Å / Num. unique obs: 3107 / CC_1/2: 0.547 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.29→48.52 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2638	1546	4.936 %	RANDOM
R_work	0.2184	29773	-	-
all	0.221	-	-	-
obs	-	29773	95.14 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 45.408 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.004 Å²	0.007 Å²	-0.005 Å²
2-	-	0.014 Å²	-0.002 Å²
3-	-	-	-0.008 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→48.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4040	0	57	149	4246

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	4162
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4160
X-RAY DIFFRACTION	r_angle_refined_deg	0.62	1.839	5618
X-RAY DIFFRACTION	r_angle_other_deg	0.247	1.755	9556
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.596	5	504
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.076	5.5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.868	10	772
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	9.794	10	172
X-RAY DIFFRACTION	r_chiral_restr	0.033	0.2	664
X-RAY DIFFRACTION	r_chiral_restr_other	0.191	0.2	4
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4830
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	954
X-RAY DIFFRACTION	r_nbd_refined	0.201	1	926
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	1	3579
X-RAY DIFFRACTION	r_nbtor_refined	0.167	1	2069
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.067	1	1960
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	1	164
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.029	1	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.176	1	10
X-RAY DIFFRACTION	r_nbd_other	0.154	1	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.118	1	5
X-RAY DIFFRACTION	r_mcbond_it	4.083	4.245	2028
X-RAY DIFFRACTION	r_mcbond_other	4.073	4.245	2028
X-RAY DIFFRACTION	r_mcangle_it	5.667	7.654	2528
X-RAY DIFFRACTION	r_mcangle_other	5.666	7.654	2529
X-RAY DIFFRACTION	r_scbond_it	5.984	5.006	2134
X-RAY DIFFRACTION	r_scbond_other	5.982	5.008	2135
X-RAY DIFFRACTION	r_scangle_it	8.982	8.892	3090
X-RAY DIFFRACTION	r_scangle_other	8.981	8.893	3091
X-RAY DIFFRACTION	r_lrange_it	10.684	52.52	16838
X-RAY DIFFRACTION	r_lrange_other	10.685	52.491	16777

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.29-2.349	0.34	102	0.333	2244	X-RAY DIFFRACTION	95.3271
2.349-2.414	0.361	111	0.328	2149	X-RAY DIFFRACTION	95.7627
2.414-2.483	0.34	123	0.302	2105	X-RAY DIFFRACTION	96.8696
2.483-2.56	0.295	125	0.272	2090	X-RAY DIFFRACTION	97.7062
2.56-2.643	0.279	108	0.242	1960	X-RAY DIFFRACTION	97.824
2.643-2.736	0.26	83	0.237	1999	X-RAY DIFFRACTION	97.7465
2.736-2.839	0.313	100	0.23	1880	X-RAY DIFFRACTION	97.8744
2.839-2.954	0.282	88	0.225	1813	X-RAY DIFFRACTION	97.8888
2.954-3.085	0.27	64	0.208	1784	X-RAY DIFFRACTION	98.2456
3.085-3.235	0.236	80	0.21	1660	X-RAY DIFFRACTION	98.6395
3.235-3.409	0.3	80	0.196	1584	X-RAY DIFFRACTION	97.9976
3.409-3.615	0.208	70	0.192	1300	X-RAY DIFFRACTION	84.5157
3.615-3.863	0.252	56	0.196	1081	X-RAY DIFFRACTION	74.6553
3.863-4.17	0.232	54	0.186	1053	X-RAY DIFFRACTION	78.678
4.17-4.565	0.268	75	0.184	1188	X-RAY DIFFRACTION	98.749
4.565-5.098	0.198	69	0.162	1090	X-RAY DIFFRACTION	99.2295
5.098-5.876	0.259	54	0.209	976	X-RAY DIFFRACTION	98.9433
5.876-7.17	0.243	53	0.238	801	X-RAY DIFFRACTION	99.3023
7.17-10.031	0.2	26	0.182	655	X-RAY DIFFRACTION	99.4161
10.031-48.52	0.375	25	0.326	355	X-RAY DIFFRACTION	97.9381

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