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

ID or keywords:

Entry

Database: PDB / ID: 4ibi

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: 1.473 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	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_ncs_dom_lim / 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 / _pdbx_database_related.db_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	4ibi.cif.gz	130 KB	Display	PDBx/mmCIF format
PDB format	pdb4ibi.ent.gz	101.5 KB	Display	PDB format
PDBx/mmJSON format	4ibi.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ibi_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4ibi_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4ibi_validation.xml.gz	16.2 KB	Display
Data in CIF	4ibi_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibi ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibi	HTTPS FTP

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Related structure data

Related structure data	4ibbC 4ibcC 4ibdC 4ibeC 4ibfC 4ibgC 4ibjC 4ibkC 4ibh PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4ibb-1 7jtz-1 4ibd-2 4ibb-2 4ibk-2 4ibk-1 6o56-1 4ibf-2 3hwj-2 6mc1-1 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

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

1

A: Polymerase cofactor VP35

hetero molecules

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

2

B: Polymerase cofactor VP35

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.302, 65.451, 72.653
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 218 - 339 / Label seq-ID: 7 - 128

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#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-1D8 / 3-{(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-4-hydroxy-5-oxo-3-[3-(trifluoromethyl)benzoyl]-2,5-dihydro-1H-pyrrol-1-yl}benzoic acid Mass: 545.848 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₆H₁₅ClF₃NO₇
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.15 Å³/Da / Density % sol: 42.68 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium citrate, pH5.5, 15% PEG3350, 10%DMS, 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: 0.9793376 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

Wavelength: 0.9793376 Å / Relative weight: 1

Reflection

Resolution: 1.46→50 Å / Num. obs: 40626 / % possible obs: 93.9 % / Redundancy: 7.9 % / R_merge(I) obs: 0.08 / Net I/σ(I): 6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.46-1.49	4.7	0.541	1	33.3
1.49-1.51	5.4	0.488	1	78.2
1.51-1.54	6.1	0.499	1	82.9
1.54-1.57	6.3	0.491	1	89
1.57-1.61	6.5	0.46	1	94.7
1.61-1.64	6.8	0.428	1	98.1
1.64-1.69	7.2	0.42	1	99.9
1.69-1.73	7.7	0.369	1	100
1.73-1.78	8.2	0.346	1	100
1.78-1.84	8.6	0.315	1	100
1.84-1.91	8.8	0.264	1	100
1.91-1.98	8.8	0.206	1	100
1.98-2.07	8.9	0.156	1	100
2.07-2.18	8.9	0.127	1	100
2.18-2.32	8.8	0.111	1	100
2.32-2.5	8.8	0.097	1	100
2.5-2.75	8.7	0.087	1	100
2.75-3.15	8.7	0.075	1	100
3.15-3.96	8.4	0.054	1	100
3.96-50	8.1	0.045	1	99.4

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.473→41.907 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.22 / SU R Cruickshank DPI: 0.0882 / σ(F): 1.34 / Phase error: 33.57 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection
R_free	0.2372	2055	5.08 %
R_work	0.1898	-	-
obs	0.1922	40482	96.25 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.6474 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.473→41.907 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1938	0	76	259	2273

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2178
X-RAY DIFFRACTION	f_angle_d	1.346	2998
X-RAY DIFFRACTION	f_dihedral_angle_d	15.456	899
X-RAY DIFFRACTION	f_chiral_restr	0.094	323
X-RAY DIFFRACTION	f_plane_restr	0.008	393

Refine LS restraints NCS

Ens-ID: 1 / Number: 160 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

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 (%)
1.4734-1.5077	0.3673	107	0.3255	2017	X-RAY DIFFRACTION	76
1.5077-1.5454	0.3799	127	0.329	2132	X-RAY DIFFRACTION	83
1.5454-1.5872	0.3967	136	0.3352	2345	X-RAY DIFFRACTION	90
1.5872-1.6339	0.3688	134	0.3212	2538	X-RAY DIFFRACTION	97
1.6339-1.6867	0.3618	152	0.284	2634	X-RAY DIFFRACTION	100
1.6867-1.7469	0.3252	115	0.2512	2637	X-RAY DIFFRACTION	100
1.7469-1.8169	0.3581	147	0.238	2640	X-RAY DIFFRACTION	100
1.8169-1.8996	0.2466	134	0.2049	2632	X-RAY DIFFRACTION	100
1.8996-1.9997	0.2466	136	0.1953	2626	X-RAY DIFFRACTION	100
1.9997-2.125	0.2272	136	0.1741	2675	X-RAY DIFFRACTION	100
2.125-2.2891	0.2202	141	0.1728	2641	X-RAY DIFFRACTION	100
2.2891-2.5194	0.2278	117	0.1695	2714	X-RAY DIFFRACTION	100
2.5194-2.8839	0.2211	165	0.1836	2661	X-RAY DIFFRACTION	100
2.8839-3.6331	0.2322	157	0.1693	2707	X-RAY DIFFRACTION	100
3.6331-41.9243	0.1849	151	0.1616	2828	X-RAY DIFFRACTION	99

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	6.5591	0.9057	-0.8567	3.1066	0.1845	3.2902	-0.156	0.3154	-0.8746	-0.1106	0.1038	0.1301	0.5122	-0.1873	-0.0125	0.1882	-0.0189	-0.0095	0.105	-0.045	0.2187	2.6448	22.3665	-12.0442
2	4.1281	-0.5079	-0.572	0.5974	-0.2584	1.9	-0.0206	0.0467	-0.1297	0.0034	0.0449	0.0506	-0.0347	-0.0932	-0.0155	0.0759	-0.0042	0.0072	0.0098	-0.0241	0.0651	3.1189	29.0505	-8.3083
3	3.6053	-0.4839	-1.3774	0.261	-0.5279	4.9291	0.259	0.1482	0.6873	0.038	0.0596	0.0565	-0.5906	-0.1652	-0.1926	0.1593	-0.0078	0.0094	0.0659	0.0068	0.2186	4.624	37.1095	-6.3112
4	6.2074	-1.6825	-0.5614	1.273	-0.158	4.7258	-0.4065	-0.6967	-0.7241	0.1694	0.246	0.1719	0.6859	0.0336	0.0979	0.206	0.0043	0.0258	0.1783	0.0432	0.1877	8.6903	20.6997	9.3741
5	2.0299	1.1431	0.9791	0.9058	-0.3466	4.4646	-0.0451	-0.0811	0.0546	-0.0706	-0.0364	0.088	-0.171	0.1816	0.0829	0.0898	-0.0137	-0.014	0.1164	0.0043	0.0979	13.2299	31.5613	7.3102
6	5.2926	-2.5871	1.8592	7.0549	-3.0051	7.3347	0.0537	-0.1795	0.3644	-0.0071	0.0935	0.3954	-0.4205	0.2485	-0.1248	0.1033	-0.0336	0.036	0.103	-0.055	0.1546	7.407	32.0537	6.2139
7	4.3507	-0.6736	-0.2878	4.2737	-3.102	2.8889	-0.0234	-0.5439	-0.3047	0.1878	0.0221	0.0967	0.325	0.2726	-0.0371	0.1538	-0.0087	0.0208	0.1834	-0.0125	0.1267	10.8825	27.1947	11.5468
8	2.0245	-0.7831	3.2392	0.5564	-0.8571	5.7862	0.0789	-0.745	-0.3793	0.6303	-0.487	-0.8102	0.791	0.4845	0.2587	0.4595	0.0459	-0.127	0.5341	0.1933	0.3762	9.3862	19.7148	40.551
9	2.8482	0.5313	-0.4861	0.8334	0.1016	1.9517	-0.0268	-0.0091	-0.6473	-0.0369	0.0184	-0.0645	0.2169	0.0685	-0.0372	0.1578	0.0094	0.0007	0.0557	0.0081	0.189	-5.4796	23.9472	30.0933
10	3.1964	-0.1014	-1.513	0.2026	0.2147	2.6763	0.059	-0.1698	0.3211	0.0051	0.0446	-0.0529	-0.2342	0.1173	-0.112	0.1211	-0.0146	0.003	0.0817	-0.0169	0.1405	-2.5284	35.0339	32.9492
11	4.3465	2.8556	2.363	2.9364	3.4333	4.6277	0.0209	0.3933	-0.5225	0.1376	0.359	-0.2298	0.2031	0.2754	-0.1149	0.1494	0.047	-0.0169	0.1524	-0.0612	0.1744	-3.4431	23.4835	13.5681
12	2.9797	-2.7777	0.0323	4.5799	1.6221	4.5842	-0.1376	0.285	-0.7017	0.2895	0.0202	0.2433	0.7634	-0.4223	0.0614	0.1961	-0.0666	0.0185	0.1183	-0.0366	0.228	-15.8019	21.2495	17.1587
13	3.2174	0.3889	0.1126	1.976	0.8182	3.1141	-0.0083	0.3023	0.3113	0.0843	-0.0634	-0.1059	-0.464	0.256	-0.11	0.1241	-0.0392	0.003	0.1084	0.0727	0.1693	-9.3267	36.529	13.2649
14	4.1119	0.6569	0.7543	2.1596	0.6364	5.9132	0.1019	0.2885	0.1588	0.1768	0.0868	-0.2906	0.111	0.2812	-0.0291	0.08	-0.0017	-0.001	0.0562	0.0228	0.1253	-8.9074	29.8585	14.7338

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 269 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 270 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 319 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 320 through 330 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 331 through 340 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 214 through 220 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 221 through 252 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 253 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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