PDB-4ibg: Ebola virus VP35 bound to small molecule

ID or keywords:

Entry

Database: PDB / ID: 4ibg

Title

Ebola virus VP35 bound to small molecule

Components

Polymerase cofactor VP35

Keywords

TRANSCRIPTION/TRANSCRIPTION inhibitor / interferon inhibitor domain / TRANSCRIPTION-TRANSCRIPTION inhibitor complex

Function / homology

Function and homology information

suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity ...
Similarity search - Function

Biological species

Ebola virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.413 Å

Authors

Brown, C.S. / Leung, D.W. / Xu, W. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / Stubbs, A.J. / Peterson, D.S. / Binning, J.M. / Amarasinghe, G.K.

Citation

Journal: J.Mol.Biol. / Year: 2014
Title: In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity.
Authors: Brown, C.S. / Lee, M.S. / Leung, D.W. / Wang, T. / Xu, W. / Luthra, P. / Anantpadma, M. / Shabman, R.S. / Melito, L.M. / Macmillan, K.S. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / ...

History

Deposition	Dec 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Jul 17, 2019	Group: Data collection / Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ibg.cif.gz	124.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ibg.ent.gz	97.6 KB	Display	PDB format
PDBx/mmJSON format	4ibg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ibg_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4ibg_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4ibg_validation.xml.gz	15.8 KB	Display
Data in CIF	4ibg_validation.cif.gz	21.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibg ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibg	HTTPS FTP

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Related structure data

Related structure data	4ibbC 4ibcC 4ibdC 4ibeC 4ibfC 4ibiC 4ibjC 4ibkC 4ibh PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4ibd-d 4ibk-d 4ibe-d 4ibf-d 6ya0-2 4ibi-d 1vq1-2 4ibj-d 4ibb-d 5cui-d Search similar-shape structures by Omokage search (details) 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 (7)

Deposited unit

A: Polymerase cofactor VP35

B: Polymerase cofactor VP35

hetero molecules

30.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	51.474, 65.937, 72.480
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Polymerase cofactor VP35 Mass: 14210.523 Da / Num. of mol.: 2 / Fragment: unp residues 215-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus / Strain: Mayinga-76 / Gene: VP35 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127

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Non-polymers , 5 types, 223 molecules

#2: Chemical	ChemComp-1D6 / {4-[(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-4-hydroxy-3-(3-methylbenzoyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid Mass: 505.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₂₀ClNO₇
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium citrate, pH5.5, 15% PEG3350, 10%DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.979237 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979237 Å / Relative weight: 1

Reflection

Resolution: 1.41→50 Å / Num. obs: 47377 / % possible obs: 98.8 % / Redundancy: 7.6 % / R_merge(I) obs: 0.1 / Net I/σ(I): 8.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.41-1.43	3.8	0.74	1	87.3
1.43-1.46	4.6	0.645	1	93.8
1.46-1.49	5.5	0.695	1	98.8
1.49-1.52	6.4	0.611	1	99.7
1.52-1.55	7.4	0.564	1	100
1.55-1.59	7.8	0.484	1	100
1.59-1.63	8.1	0.357	1	99.9
1.63-1.67	8.2	0.318	1	100
1.67-1.72	8.3	0.263	1	100
1.72-1.78	8.3	0.222	1	100
1.78-1.84	8.3	0.177	1	100
1.84-1.91	8.4	0.152	1	100
1.91-2	8.4	0.122	1	100
2-2.11	8.4	0.101	1	100
2.11-2.24	8.4	0.088	1	99.9
2.24-2.41	8.4	0.093	1	100
2.41-2.65	8.3	0.086	1	99.9
2.65-3.04	8.3	0.073	1	99.9
3.04-3.83	8	0.06	1	99.9
3.83-50	7.7	0.051	1	97.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
SCALEPACK		data scaling
MOLREP		phasing
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.413→31.759 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.14 / σ(F): 1.33 / Phase error: 22.99 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection
R_free	0.1996	2385	5.05 %
R_work	0.1783	-	-
obs	0.1794	47199	98.43 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 16.9456 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.413→31.759 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1910	0	115	213	2238

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2123
X-RAY DIFFRACTION	f_angle_d	1.162	2902
X-RAY DIFFRACTION	f_dihedral_angle_d	13.729	828
X-RAY DIFFRACTION	f_chiral_restr	0.067	308
X-RAY DIFFRACTION	f_plane_restr	0.006	376

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 (%)
1.4132-1.4421	0.3065	123	0.299	2245	X-RAY DIFFRACTION	85
1.4421-1.4734	0.2863	134	0.2657	2500	X-RAY DIFFRACTION	95
1.4734-1.5077	0.3069	145	0.2787	2563	X-RAY DIFFRACTION	97
1.5077-1.5454	0.2284	135	0.2393	2624	X-RAY DIFFRACTION	100
1.5454-1.5872	0.2577	129	0.2342	2641	X-RAY DIFFRACTION	99
1.5872-1.6339	0.2093	151	0.1814	2641	X-RAY DIFFRACTION	100
1.6339-1.6866	0.2175	126	0.1685	2657	X-RAY DIFFRACTION	100
1.6866-1.7469	0.1925	148	0.1637	2656	X-RAY DIFFRACTION	100
1.7469-1.8169	0.2099	143	0.1642	2667	X-RAY DIFFRACTION	100
1.8169-1.8995	0.2108	133	0.1497	2665	X-RAY DIFFRACTION	100
1.8995-1.9997	0.1899	123	0.1496	2685	X-RAY DIFFRACTION	100
1.9997-2.1249	0.1671	139	0.1465	2674	X-RAY DIFFRACTION	100
2.1249-2.289	0.18	156	0.1506	2660	X-RAY DIFFRACTION	100
2.289-2.5192	0.1729	135	0.1561	2702	X-RAY DIFFRACTION	100
2.5192-2.8835	0.2038	154	0.1684	2712	X-RAY DIFFRACTION	100
2.8835-3.6321	0.1732	173	0.1697	2704	X-RAY DIFFRACTION	100
3.6321-31.7672	0.206	138	0.1968	2818	X-RAY DIFFRACTION	98

Refinement TLS params.

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

ID	L11 (°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)
1	4.9017	0.6154	-0.7339	1.7798	0.3512	2.599	-0.0825	0.3879	-0.554	-0.0892	0.0077	0.2185	0.2041	-0.1879	0.0225	0.1212	-0.0036	-0.0031	0.0842	-0.0347	0.16	2.449	22.7346	-12.1713
2	3.343	-1.3964	0.2658	0.9914	-0.3075	1.3187	-0.1667	-0.055	-0.3711	0.0495	0.0976	0.0933	0.1271	-0.0252	0.0305	0.0992	0.0042	0.0104	0.0496	-0.0057	0.0851	6.1231	26.1087	-4.2094
3	8.3182	2.9389	-5.1873	2.3843	-2.8889	5.941	0.0676	0.4259	0.2515	-0.0231	0.1081	0.1763	-0.0907	-0.1775	-0.1345	0.0898	0.012	-0.0132	0.0786	0.0123	0.0731	-0.2375	33.2002	-13.7206
4	2.9275	0.5225	-3.1895	1.1492	0.3996	5.7394	0.1881	0.2106	0.508	0.0788	0.1451	0.2154	-0.2951	0.0255	-0.1637	0.0982	0.0075	0.0139	0.0751	0.0405	0.1352	8.0167	37.1987	-9.9935
5	3.2621	-1.8848	0.8978	5.0571	-2.7895	4.2242	-0.0252	-0.0744	0.1284	0.1911	-0.0812	-0.1033	-0.081	-0.0262	0.0551	0.0657	-0.0065	0.0198	0.0702	-0.0195	0.0766	2.1002	30.4902	4.6427
6	5.4312	-2.0121	-2.9053	5.3935	1.3495	2.1644	-0.2011	-0.4426	-0.4655	0.5511	0.1534	-0.1252	0.3697	0.2124	0.033	0.2207	0.0388	0.0121	0.1339	0.0527	0.1378	14.3022	19.848	6.9999
7	3.8049	-0.1815	-0.9701	4.7631	2.2278	3.2913	0.0524	-0.0095	-0.2977	0.0244	-0.0077	-0.5183	0.5682	0.3581	0.0392	0.1358	0.0518	-0.0079	0.1162	0.0071	0.1327	18.9431	24.3968	3.2188
8	2.6544	-0.1498	1.0091	0.417	-0.7363	3.2519	-0.2318	-0.2808	0.5505	0.0931	-0.0167	-0.0264	-0.5393	0.0672	0.0414	0.1519	0.0179	-0.0239	0.0593	-0.0533	0.1164	10.1178	36.2761	10.4687
9	3.202	0.2115	0.663	5.2592	-1.6916	4.0067	-0.0163	-0.0301	0.2289	0.3081	-0.014	-0.057	-0.231	-0.0327	-0.0012	0.107	0.0031	0.0101	0.062	-0.012	0.1101	7.3032	33.2993	5.4689
10	1.6855	-0.0475	-0.604	2.9237	-0.7357	4.7509	0.0358	-0.229	-0.1352	-0.0444	-0.0054	0.0541	0.4683	-0.0935	0.0503	0.1296	-0.0231	-0.0033	0.132	0.0245	0.0987	11.007	26.8277	11.6309
11	4.9473	0.1047	-1.1853	2.0727	-0.1759	0.5163	-0.1288	-0.3883	-0.691	0.119	0.0905	-0.4096	0.1237	0.1968	0.0013	0.1286	0.0169	-0.0183	0.1334	0.0444	0.2028	-2.4389	22.1514	35.1417
12	4.2119	1.6659	0.3525	0.9748	0.3218	1.373	-0.1031	-0.0066	-0.3701	-0.0172	0.052	-0.0531	0.1007	0.0312	0.0555	0.1024	-0.0005	0.0086	0.046	0.0003	0.0895	-6.2507	25.5609	27.2826
13	7.0418	-2.2878	-3.5853	1.8476	2.1828	4.085	0.0281	-0.3526	0.1915	0.0583	0.1263	-0.1511	-0.0557	0.0619	-0.0829	0.0771	0.0027	-0.0054	0.0706	0.0016	0.0484	0.582	32.6624	36.6888
14	2.7162	0.1458	-2.8046	0.2267	-0.4019	3.9815	0.2261	-0.1455	0.3141	0.0032	0.042	-0.0385	-0.323	0.0221	-0.1308	0.1043	0.012	0.0084	0.0831	-0.0256	0.1205	-7.9506	36.7443	33.4817
15	1.9908	0.837	0.1765	1.5813	1.1998	2.6396	-0.1406	0.1694	0.0857	-0.1594	0.0562	0.1224	-0.0361	0.0566	0.0636	0.0855	0.0056	0.0017	0.0464	0.0022	0.0972	-4.9671	27.8977	18.0374
16	4.0361	0.3776	-0.4914	4.0201	-3.1895	4.7289	0.2495	-0.0274	-0.2375	0.1369	-0.1216	0.6267	0.62	-0.148	0.0661	0.1629	-0.0316	0.0258	0.1191	-0.0282	0.1966	-18.9392	24.3033	19.851
17	3.122	0.3787	1.4424	1.1174	2.1012	4.1038	-0.1168	0.2539	0.3362	-0.0672	-0.0141	0.1527	-0.5304	0.0705	0.0614	0.1076	-0.0012	-0.0079	0.0709	0.0371	0.1146	-10.2167	35.9714	13.2651
18	2.2709	0.0271	0.1341	2.5829	0.4588	3.3401	0.0483	0.1727	0.0933	0.0199	-0.0716	0.0031	0.0992	-0.0809	0.0392	0.0898	0.0028	0.0165	0.0674	0.007	0.1048	-9.0459	30.154	14.7373

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 218 through 231 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 232 through 252 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 253 through 269 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 270 through 283 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 284 through 299 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 300 through 304 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 305 through 310 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 311 through 319 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 320 through 329 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 330 through 340 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 218 through 231 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 232 through 252 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 253 through 269 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 270 through 283 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 284 through 304 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 305 through 310 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 311 through 319 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 320 through 340 )

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