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

ID or keywords:

Entry

Database: PDB / ID: 4ibc

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

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 IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of protein sumoylation / viral transcription / molecular sequestering activity ...
Similarity search - Function

Biological species

Ebola virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.745 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	4ibc.cif.gz	116.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ibc.ent.gz	90.7 KB	Display	PDB format
PDBx/mmJSON format	4ibc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ibc_validation.pdf.gz	1007.8 KB	Display	wwPDB validaton report
Full document	4ibc_full_validation.pdf.gz	1010.8 KB	Display
Data in XML	4ibc_validation.xml.gz	14.8 KB	Display
Data in CIF	4ibc_validation.cif.gz	20.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibc ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibc	HTTPS FTP

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Related structure data

Related structure data	4ibbC 4ibdC 4ibeC 4ibfC 4ibgC 4ibiC 4ibjC 4ibkC 4ibh PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4ibf-1 3fke-1 3l29-1 4ibe-1 4ibk-1 5bpv-2 4ibj-2 4ibd-1 5bpv-1 4ibb-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
14.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.947, 65.902, 72.040
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-12G / {4-[(2R)-3-(2-chlorobenzoyl)-2-(2-chlorophenyl)-4-hydroxy-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid Mass: 482.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₅H₁₇Cl₂NO₅
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.17 Å³/Da / Density % sol: 43.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM magnesium acetate, pH7.5, 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: 18-ID / Wavelength: 0.9793378 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

Wavelength: 0.9793378 Å / Relative weight: 1

Reflection

Resolution: 1.74→50 Å / Num. obs: 25426 / % possible obs: 98.7 % / Redundancy: 6.4 % / R_merge(I) obs: 0.125 / Net I/σ(I): 7.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.74-1.77	3.9	0.696	1	90.3
1.77-1.8	4.4	0.642	1	92.7
1.8-1.84	5.2	0.701	1	98.7
1.84-1.87	5.7	0.685	1	99.8
1.87-1.92	6.2	0.627	1	99.9
1.92-1.96	6.8	0.522	1	100
1.96-2.01	7	0.42	1	100
2.01-2.06	7.2	0.324	1	99.9
2.06-2.12	7.2	0.274	1	100
2.12-2.19	7.2	0.234	1	100
2.19-2.27	7.1	0.221	1	100
2.27-2.36	6.9	0.229	1	99.9
2.36-2.47	7.1	0.158	1	100
2.47-2.6	6.8	0.161	1	100
2.6-2.76	7	0.112	1	100
2.76-2.98	6.9	0.104	1	100
2.98-3.27	6.7	0.085	1	99.8
3.27-3.75	6.4	0.06	1	99.9
3.75-4.72	6.4	0.048	1	99.1
4.72-50	6	0.047	1	93.8

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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: 1.745→32.951 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / SU R Cruickshank DPI: 0.1417 / σ(F): 1.34 / Phase error: 29.97 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection
R_free	0.2499	1290	5.11 %
R_work	0.1908	-	-
obs	0.1938	25241	97.82 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.63 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.745→32.951 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1910	0	70	198	2178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2068
X-RAY DIFFRACTION	f_angle_d	1.025	2823
X-RAY DIFFRACTION	f_dihedral_angle_d	13.121	814
X-RAY DIFFRACTION	f_chiral_restr	0.06	306
X-RAY DIFFRACTION	f_plane_restr	0.004	372

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 (%)
1.7449-1.8148	0.3843	116	0.3012	2348	X-RAY DIFFRACTION	88
1.8148-1.8974	0.2857	134	0.2476	2646	X-RAY DIFFRACTION	98
1.8974-1.9974	0.3191	143	0.2396	2679	X-RAY DIFFRACTION	100
1.9974-2.1225	0.2207	138	0.1844	2682	X-RAY DIFFRACTION	100
2.1225-2.2864	0.2304	156	0.1751	2674	X-RAY DIFFRACTION	100
2.2864-2.5164	0.2319	157	0.196	2657	X-RAY DIFFRACTION	99
2.5164-2.8803	0.2436	140	0.1858	2738	X-RAY DIFFRACTION	100
2.8803-3.6282	0.2433	163	0.1779	2725	X-RAY DIFFRACTION	100
3.6282-32.9569	0.2431	143	0.1727	2802	X-RAY DIFFRACTION	97

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	5.5959	-0.3602	-1.6694	2.4693	-0.5616	3.0351	-0.2372	1.2069	-1.3321	-0.1611	0.4249	0.1649	0.4003	-0.56	0.1736	0.1738	-0.0043	-0.0239	0.2032	-0.0959	0.2295	2.7617	22.9201	-12.2541
2	3.8998	-0.8793	-0.6878	0.6488	-0.0344	1.7979	-0.2579	0.0278	-0.8863	0.211	0.1075	0.1492	0.3159	-0.0482	0.065	0.1185	0.0126	0.0097	0.0855	-0.01	0.1219	6.206	26.1149	-4.0554
3	3.3792	0.7557	-2.1352	0.8502	-0.9874	4.2527	0.1402	0.2359	0.3042	-0.17	0.0568	0.2927	-0.0352	-0.0118	-0.051	0.1091	0.0287	0.0026	0.1311	0.0029	0.1007	-1.0576	32.7775	-12.8392
4	3.9651	0.4854	-2.8644	0.4447	0.0765	4.9773	0.3608	0.5336	0.5997	0.0395	0.1188	0.1949	-0.3437	-0.1251	-0.1377	0.1362	-0.0001	0.0268	0.131	0.0419	0.1723	7.941	37.6021	-10.5325
5	4.013	-0.3963	0.4325	0.3734	-0.2928	4.3189	-0.0493	-0.6203	-0.1032	0.21	0.0913	-0.026	0.4119	-0.4831	-0.0116	0.2167	-0.0631	-0.0098	0.1881	-0.0038	0.1507	5.0457	27.7006	5.3888
6	3.5084	0.1764	0.3869	1.832	0.6607	4.6103	0.1884	-0.0719	0.2623	0.1534	-0.228	-0.0789	-0.1255	-0.1	-0.0402	0.1751	-0.0303	0.0068	0.0887	-0.0174	0.0972	11.2147	32.0058	6.8959
7	3.8922	-0.6388	-0.9228	0.9665	0.5151	6.3	0.2963	-0.3429	-0.4504	0.2056	-0.1451	0.2162	0.566	0.4397	0.0614	0.2234	-0.0355	-0.016	0.1858	-0.0026	0.175	11.3232	26.5142	11.7648
8	2.8542	0.5234	-0.6911	1.0276	0.2278	2.2567	0.0996	-0.1757	-0.813	-0.0385	-0.0007	-0.1858	0.2199	0.1121	0.0832	0.1197	-0.0021	-0.0167	0.0784	0.0367	0.1871	-4.7033	24.2293	31.0644
9	3.533	0.1478	-0.5883	0.6238	0.408	2.8375	0.0789	-0.2402	0.2944	-0.0338	0.0156	-0.096	-0.2295	0.0727	-0.1132	0.0788	-0.0015	0.0066	0.0798	-0.0104	0.1127	-2.5089	35.3374	32.7102
10	3.982	-0.2668	0.0032	1.9547	-0.2845	4.5824	0.1163	0.3781	-0.1418	-0.1412	-0.1193	0.0178	0.2668	0.1015	0.0248	0.1718	0.0197	0.0055	0.1336	-0.0223	0.0996	-10.7939	27.7412	15.0571

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 268 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 269 through 283 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 284 through 304 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 305 through 329 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 330 through 340 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 218 through 252 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 253 through 292 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 293 through 340 )

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