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

ID or keywords:

Entry

Database: PDB / ID: 4ibj

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 / positive regulation of protein sumoylation / viral transcription / molecular sequestering activity / viral genome replication ...
Similarity search - Function

Biological species

Ebola virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.54 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

-
Download

PDBx/mmCIF format	4ibj.cif.gz	122.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ibj.ent.gz	96.8 KB	Display	PDB format
PDBx/mmJSON format	4ibj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	4ibbC 4ibcC 4ibdC 4ibeC 4ibfC 4ibgC 4ibiC 4ibkC 4ibh PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4ibk-1 4ibe-2 2xqx-1 4ibc-2 4ibd-1 4ibf-1 4ibb-1 4ibk-2 4ibe-1 3lgl-d 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

-
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
14.7 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)	51.257, 66.346, 72.659
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-1D9 / 3-{(5S)-3-hydroxy-2-oxo-4-[3-(trifluoromethyl)benzoyl]-5-[3-(trifluoromethyl)phenyl]-2,5-dihydro-1H-pyrrol-1-yl}benzoic acid Mass: 535.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₆H₁₅F₆NO₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.41 %
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

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-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: 1.54→50 Å / Num. obs: 36721 / % possible obs: 98.1 % / Redundancy: 6.7 % / R_merge(I) obs: 0.082 / Net I/σ(I): 7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.54-1.57	5.1	0.652	1	83.1
1.57-1.6	5.6	0.623	1	88.9
1.6-1.63	5.8	0.549	1	93.8
1.63-1.66	5.9	0.536	1	97.6
1.66-1.69	6.2	0.489	1	99.1
1.69-1.73	6.4	0.433	1	99.9
1.73-1.78	6.6	0.421	1	99.9
1.78-1.83	6.8	0.352	1	100
1.83-1.88	7	0.326	1	100
1.88-1.94	7.1	0.268	1	100
1.94-2.01	7.2	0.212	1	100
2.01-2.09	7.2	0.159	1	99.9
2.09-2.19	7.2	0.127	1	99.9
2.19-2.3	7.2	0.115	1	100
2.3-2.44	7.2	0.09	1	100
2.44-2.63	7.2	0.085	1	100
2.63-2.9	7.2	0.073	1	100
2.9-3.32	7.1	0.065	1	100
3.32-4.18	6.9	0.046	1	100
4.18-50	6.7	0.043	1	98.9

-
Phasing

Phasing	Method: molecular replacement

-
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: 1.54→35.417 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.15 / SU R Cruickshank DPI: 0.1139 / σ(F): 1.34 / Phase error: 29.75 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection
R_free	0.2294	3203	10.12 %
R_work	0.1825	-	-
obs	0.1872	31662	84.67 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.4458 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.54→35.417 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1924	0	76	309	2309

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2149
X-RAY DIFFRACTION	f_angle_d	1.092	2952
X-RAY DIFFRACTION	f_dihedral_angle_d	19.286	865
X-RAY DIFFRACTION	f_chiral_restr	0.063	316
X-RAY DIFFRACTION	f_plane_restr	0.004	378

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 (%)
1.5395-1.5625	0.2286	61	0.2177	599	X-RAY DIFFRACTION	41
1.5625-1.5869	0.2395	94	0.2047	698	X-RAY DIFFRACTION	50
1.5869-1.6129	0.213	79	0.1948	821	X-RAY DIFFRACTION	56
1.6129-1.6408	0.2647	111	0.1996	825	X-RAY DIFFRACTION	60
1.6408-1.6706	0.2614	96	0.2064	946	X-RAY DIFFRACTION	65
1.6706-1.7027	0.2282	108	0.2062	997	X-RAY DIFFRACTION	69
1.7027-1.7375	0.226	104	0.1989	1086	X-RAY DIFFRACTION	74
1.7375-1.7753	0.2946	132	0.2196	1130	X-RAY DIFFRACTION	78
1.7753-1.8166	0.3124	115	0.1959	1209	X-RAY DIFFRACTION	82
1.8166-1.862	0.2083	149	0.2091	1237	X-RAY DIFFRACTION	86
1.862-1.9123	0.2412	182	0.1955	1270	X-RAY DIFFRACTION	90
1.9123-1.9686	0.2162	183	0.2057	1372	X-RAY DIFFRACTION	96
1.9686-2.0321	0.2408	141	0.1946	1445	X-RAY DIFFRACTION	99
2.0321-2.1047	0.2509	156	0.1826	1442	X-RAY DIFFRACTION	100
2.1047-2.189	0.1856	159	0.1816	1465	X-RAY DIFFRACTION	100
2.189-2.2886	0.2738	172	0.1749	1462	X-RAY DIFFRACTION	100
2.2886-2.4092	0.2064	165	0.1682	1462	X-RAY DIFFRACTION	100
2.4092-2.5601	0.2146	137	0.1739	1485	X-RAY DIFFRACTION	100
2.5601-2.7577	0.2402	161	0.1798	1467	X-RAY DIFFRACTION	100
2.7577-3.0351	0.2117	178	0.1779	1478	X-RAY DIFFRACTION	100
3.0351-3.474	0.1999	163	0.1783	1496	X-RAY DIFFRACTION	100
3.474-4.3756	0.1912	165	0.1553	1504	X-RAY DIFFRACTION	100
4.3756-35.4263	0.2856	192	0.2002	1563	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	5.3523	-0.8173	-0.729	2.0696	-0.6132	2.3457	0.0056	0.0434	-0.4879	-0.0854	0.0491	0.1685	0.1411	-0.1299	-0.0656	0.1273	-0.0044	-0.0076	0.085	-0.0117	0.1278	3.995	24.622	-7.426
2	4.074	0.2939	-1.1451	0.3659	-0.4688	2.5446	0.0668	0.1982	0.2328	-0.0017	0.0605	0.0516	-0.1546	-0.094	-0.1575	0.1359	0.0198	0.0058	0.1056	0.012	0.1525	2.5676	35.7789	-9.4539
3	7.5944	-0.052	0.6454	4.1698	-0.6598	3.2946	-0.0231	-0.4288	-0.6653	0.1159	-0.1609	0.038	0.5921	-0.0842	0.1939	0.2238	0.0037	0.0167	0.1343	0.0064	0.1115	12.392	22.1262	7.1012
4	4.5541	-0.5697	0.9087	1.9639	-0.3427	5.9375	-0.0589	-0.309	0.12	0.0743	0.0782	0.075	-0.0722	-0.096	-0.031	0.1417	0.0145	0.0157	0.1476	-0.0364	0.1176	9.3476	31.7821	9.1397
5	7.5234	-3.1422	1.0881	4.3078	-0.4377	2.2911	0.0146	-0.3841	-0.6903	0.1549	0.0222	-0.1091	0.2201	0.2768	-0.0427	0.1586	0.0085	-0.0265	0.1763	0.0579	0.2016	-1.6482	22.5531	35.6679
6	8.1911	1.2087	0.109	1.6207	0.106	2.3104	-0.0854	-0.0065	-0.6588	-0.0376	0.0551	-0.1568	0.1309	0.0377	0.0292	0.0936	0.0041	0.0076	0.0759	-0.0092	0.1091	-5.1586	26.1483	27.3838
7	3.3644	-2.1591	-3.8384	3.0319	1.3255	5.3032	-0.0093	-0.3654	0.259	0.1212	0.1483	-0.1753	-0.0168	0.044	-0.1295	0.0876	-0.0011	-0.0223	0.1782	-0.0167	0.1048	-0.3484	33.3715	37.9436
8	7.5693	-0.1249	-6.8428	0.5676	-0.6079	8.2535	0.4134	-0.2251	0.571	0.1684	0.0605	-0.1368	-0.5182	0.0605	-0.4339	0.1461	0.0199	-0.0098	0.1288	-0.0348	0.1583	-7.8321	36.9476	33.5373
9	5.0193	0.4051	3.4634	1.2603	0.5317	2.4461	-0.162	0.0362	0.8413	-0.0798	-0.1354	0.0454	-0.478	0.4839	0.1235	0.1433	-0.0485	0.0205	0.174	-0.0603	0.2123	1.1475	37.9186	23.7901
10	8.4762	5.9043	3.0984	4.852	3.9156	5.3003	-0.2782	0.1672	-0.5786	-0.0199	0.2105	-0.0664	0.0397	-0.4117	0.0698	0.1707	0.0175	0.0148	0.2087	-0.036	0.159	-5.4612	21.6022	12.8014
11	7.3169	-4.5509	2.1868	7.1473	1.5005	4.9001	-0.0076	0.2596	-0.626	-0.1511	0.095	0.1283	0.7035	-0.3634	-0.0006	0.1909	-0.072	0.027	0.1339	-0.0273	0.132	-16.802	22.4827	18.5149
12	3.8775	0.3687	2.4853	0.756	1.6631	4.4239	-0.1449	0.3608	0.3322	-0.0819	0.0669	0.0154	-0.3966	0.1169	0.0646	0.1951	0.0114	0.0129	0.1746	0.0527	0.1963	-10.1559	35.8874	13.4561
13	7.0457	0.4469	1.7334	9.5285	5.6241	3.6514	0.0023	0.1621	0.2763	-0.5159	0.0784	-0.1983	-0.2319	0.396	-0.0592	0.1873	-0.0103	0.0414	0.1651	0.0508	0.1532	-7.1185	33.1448	17.8903
14	5.5512	-0.6153	-0.8344	4.2107	2.4238	8.5294	0.077	0.6255	-0.3762	-0.1193	0.0818	-0.0636	0.4257	0.1351	-0.1037	0.1258	-0.0062	0.0054	0.2002	-0.0036	0.1302	-10.7788	27.0741	11.5668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 217 through 252 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 253 through 292 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 293 through 310 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 311 through 340 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 217 through 231 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 232 through 253 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 254 through 269 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 270 through 283 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 284 through 292 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 293 through 299 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 300 through 310 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 311 through 319 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 320 through 329 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 330 through 340 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi