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

ID or keywords:

Entry

Database: PDB / ID: 4ibk

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 / molecular sequestering activity / positive regulation of protein sumoylation ...
Similarity search - Function

Biological species

Ebola virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 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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PDBx/mmCIF format	4ibk.cif.gz	117.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ibk.ent.gz	91.1 KB	Display	PDB format
PDBx/mmJSON format	4ibk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibk ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibk	HTTPS FTP

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Related structure data

Related structure data	4ibbC 4ibcC 4ibdC 4ibeC 4ibfC 4ibgC 4ibiC 4ibjC 4ibh PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4ibb-1 4ibj-2 4ibi-1 3lgl-d 4ibj-1 4ibe-2 2xqx-1 4ibc-2 2w1u-1 4ibc-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

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

1

A: Polymerase cofactor VP35

hetero molecules

defined by software
15 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Polymerase cofactor VP35

hetero molecules

defined by software
14.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.222, 65.689, 72.831
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127
#2: Chemical	ChemComp-1DE / 3-{(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-3-[(5-chlorothiophen-2-yl)carbonyl]-4-hydroxy-5-oxo-2,5-dihydro-1H-pyrrol-1-yl}benzoic acid Mass: 518.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₁₃Cl₂NO₇S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 216 / 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: 42.94 %
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: 0.9791209 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

Wavelength: 0.9791209 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 21610 / % possible obs: 99.9 % / Redundancy: 6.9 % / R_merge(I) obs: 0.125 / Net I/σ(I): 7.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.85-1.88	5.6	0.481	1	99.5
1.88-1.92	6.1	0.404	1	99.7
1.92-1.95	6.8	0.368	1	100
1.95-1.99	7	0.27	1	99.8
1.99-2.04	7.1	0.263	1	99.8
2.04-2.08	7.1	0.3	1	99.9
2.08-2.14	7.1	0.214	1	100
2.14-2.19	7.2	0.186	1	99.9
2.19-2.26	7.2	0.212	1	99.9
2.26-2.33	7.2	0.187	1	100
2.33-2.41	7.2	0.153	1	100
2.41-2.51	7.2	0.158	1	100
2.51-2.63	7.2	0.128	1	100
2.63-2.76	7.2	0.126	1	100
2.76-2.94	7.1	0.109	1	100
2.94-3.16	7.1	0.103	1	100
3.16-3.48	7.1	0.107	1	100
3.48-3.99	7	0.089	1	100
3.99-5.02	6.7	0.075	1	100
5.02-50	6.4	0.093	1	99.8

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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		refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→41.898 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.18 / SU R Cruickshank DPI: 0.1737 / σ(F): 1.34 / Phase error: 29.49 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection
R_free	0.2414	1088	5.1 %
R_work	0.1925	-	-
obs	0.1949	21347	98.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.0469 Å²

	B_aniso -1	B_aniso -2
1-	-0.01 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.85→41.898 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1917	0	82	216	2215

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2072
X-RAY DIFFRACTION	f_angle_d	1.183	2824
X-RAY DIFFRACTION	f_dihedral_angle_d	16.048	820
X-RAY DIFFRACTION	f_chiral_restr	0.061	304
X-RAY DIFFRACTION	f_plane_restr	0.005	368

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 (%)
1.8497-1.9338	0.2948	147	0.2411	2441	X-RAY DIFFRACTION	97
1.9338-2.0358	0.2709	114	0.2105	2489	X-RAY DIFFRACTION	98
2.0358-2.1633	0.2268	136	0.1872	2476	X-RAY DIFFRACTION	99
2.1633-2.3304	0.2361	146	0.1854	2498	X-RAY DIFFRACTION	98
2.3304-2.5648	0.2576	155	0.1893	2487	X-RAY DIFFRACTION	99
2.5648-2.9359	0.2381	127	0.1989	2547	X-RAY DIFFRACTION	99
2.9359-3.6986	0.247	138	0.1834	2600	X-RAY DIFFRACTION	100
3.6986-41.9084	0.2165	125	0.1866	2721	X-RAY DIFFRACTION	100

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	4.8727	1.5488	-1.0283	1.4287	0.2441	1.69	-0.0537	0.5072	-0.5019	-0.1755	0.0544	0.0951	0.3115	-0.3302	0.0952	0.1181	-0.0167	-0.014	0.123	-0.0343	0.1753	2.3073	22.3908	-11.9209
2	3.5519	-0.7375	-1.1052	0.1813	0.1089	2.1558	-0.2586	-0.0602	-0.4672	0.0413	0.1812	0.0559	0.1093	-0.0595	0.0701	0.0983	0.0105	0.0098	0.0605	-0.0069	0.0838	6.1406	25.8493	-4.1299
3	1.8106	0.1733	-1.1129	0.1575	-0.1259	2.3883	0.0552	0.1397	0.2108	0.0222	0.0401	0.0637	-0.1881	-0.0338	-0.1028	0.1051	0.0205	-0.008	0.0868	0.0122	0.1193	2.5776	35.3968	-9.6951
4	3.8098	-1.4147	-0.1074	0.9616	0.2013	2.0151	-0.2726	-0.6079	-0.5381	0.1344	0.1643	0.1184	0.5532	-0.0704	0.0333	0.1946	0.0244	0.0235	0.1229	0.041	0.1436	9.1708	20.8048	9.0351
5	2.5397	-0.1426	-0.5638	0.9219	-0.1129	3.6292	0.0083	-0.2771	0.0967	0.0273	0.0045	0.1735	-0.0731	-0.0296	-0.0068	0.101	-0.0026	0.0048	0.0973	-0.0144	0.1009	11.0019	30.4714	7.8119
6	3.0423	-0.3176	-0.6731	0.9419	0.4375	2.4739	-0.0367	-0.2177	-0.588	0.0098	0.065	-0.2549	0.394	0.3588	0.1309	0.1507	0.0129	-0.0244	0.0933	0.0549	0.2435	-1.6209	22.0014	35.3214
7	4.0407	0.4407	-1.2052	0.0978	0.0787	2.5184	-0.0245	0.0772	-0.3593	-0.1259	0.0718	-0.0422	0.0721	-0.0346	0.0956	0.1069	-0.0091	0.0026	0.0429	-0.0046	0.0758	-6.25	25.6629	27.289
8	4.6011	-0.6215	-2.7919	0.5915	0.1759	3.8608	-0.0903	-0.437	0.1249	0.109	0.1388	-0.0611	0.1776	0.1539	-0.0586	0.0795	-0.004	-0.0067	0.123	-0.0059	0.0793	0.0637	32.7916	37.1894
9	3.2553	0.2167	-3.5125	0.097	-0.3648	3.9819	0.2701	-0.163	0.5802	0.0244	0.0821	-0.0434	-0.3445	0.0353	-0.1278	0.1141	-0.0059	0.0091	0.0953	-0.0091	0.1343	-8.0747	36.5633	33.4558
10	1.9544	0.5118	0.7107	0.8849	0.2781	4.5353	-0.1349	-0.2441	0.4459	-0.16	-0.0945	0.2516	-0.4601	0.5143	-0.0569	0.1373	-0.0473	0.0011	0.1553	-0.0275	0.155	1.11	37.7163	23.5875
11	5.4301	4.558	1.7483	6.1476	0.2826	1.9608	0.0256	0.0921	-0.5074	-0.2007	-0.0913	0.0625	0.2648	-0.0145	0.0228	0.1224	0.0246	0.001	0.0873	-0.0307	0.1232	-3.7902	23.8746	13.7889
12	1.6913	-1.3001	-0.6748	2.449	1.4294	3.6945	-0.1512	0.3273	-0.2618	0.1778	0.1888	0.0432	0.5306	-0.2231	0.1472	0.1709	-0.0406	0.0222	0.1375	-0.0271	0.1786	-15.6897	21.302	16.9587
13	0.7129	0.1497	-0.1252	0.5422	0.2777	2.3166	-0.0849	0.0201	0.3224	0.1593	-0.0632	-0.2095	-0.4763	-0.0005	-0.1385	0.1465	-0.0279	-0.0424	0.0939	0.047	0.1503	-9.7847	36.4758	12.9156
14	2.827	0.3806	-0.2193	0.6839	0.1499	4.1973	0.0363	0.2082	0.126	0.07	0.0178	-0.0339	0.0325	0.0576	-0.0225	0.0792	0.0134	0.0098	0.0853	0.0111	0.0818	-8.9971	30.0738	14.7908

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 292 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 293 through 304 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 305 through 340 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 217 through 231 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 232 through 252 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 253 through 269 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 270 through 283 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 284 through 292 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 293 through 297 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 298 through 310 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 311 through 319 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 320 through 340 )

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