PDB-6npi: Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1,...

ID or keywords:

Entry

Database: PDB / ID: 6npi

Title

Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments

Components

Epstein-Barr nuclear antigen 1

Keywords

viral protein/inhibitor / EBNA1 / DNA binding protein / Epstein-Barr Virus / viral protein / viral protein-inhibitor complex

Function / homology

Function and homology information

host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / symbiont-mediated suppression of host NF-kappaB cascade / endonuclease activity / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Epstein-Barr virus (Epstein-Barr virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.501 Å

Authors

Messick, T.E.

Funding support

United Kingdom, 1items

Citation

Journal: Sci Transl Med / Year: 2019
Title: Structure-based design of small-molecule inhibitors of EBNA1 DNA binding blocks Epstein-Barr virus latent infection and tumor growth.
Authors: Messick, T.E. / Smith, G.R. / Soldan, S.S. / McDonnell, M.E. / Deakyne, J.S. / Malecka, K.A. / Tolvinski, L. / van den Heuvel, A.P.J. / Gu, B.W. / Cassel, J.A. / Tran, D.H. / Wassermann, B.R. ...

History

Deposition	Jan 17, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6npi.cif.gz	182.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6npi.ent.gz	147 KB	Display	PDB format
PDBx/mmJSON format	6npi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6npi_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6npi_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6npi_validation.xml.gz	17.5 KB	Display
Data in CIF	6npi_validation.cif.gz	26 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/6npi ftp://data.pdbj.org/pub/pdb/validation_reports/np/6npi	HTTPS FTP

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Related structure data

Related structure data	6npmC 6nppC 1vhiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6npm-d 3kn5-2 6vh6-d 4yge-3 2af2-d 4jb2-d 3iue-3 2c4k-1 3wgn-2 4eyq-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

Deposited unit

A: Epstein-Barr nuclear antigen 1

B: Epstein-Barr nuclear antigen 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, EBNA1 is a dimer in solution

Unit cell

Length a, b, c (Å)	59.704, 67.452, 69.498
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Epstein-Barr nuclear antigen 1 / EBV nuclear antigen 1 Mass: 15306.679 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 / Gene: EBNA1, BKRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03211
#2: Chemical	ChemComp-60Q / 2-pyrrol-1-ylbenzoic acid Mass: 187.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C₁₁H₉NO₂
#3: Chemical	ChemComp-KW1 / ({2-[(4-bromo-5-methyl-1,2-oxazol-3-yl)amino]-2-oxoethyl}sulfanyl)acetic acid Mass: 309.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₉BrN₂O₄S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.29 Å³/Da / Density % sol: 46.18 % / Description: Rectangular rods
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50 mM MES, pH 6.5, and 0-100 mM NaCl, 10 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 42238 / % possible obs: 92.76 % / Redundancy: 5.2 % / B_iso Wilson estimate: 12.34 Å² / Net I/σ(I): 25.8
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3025 / % possible all: 94

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VHI

1vhi

Resolution: 1.501→30.342 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1626	2015	4.77 %
R_work	0.141	-	-
obs	0.1421	42238	92.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.501→30.342 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2095	0	30	372	2497

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2316
X-RAY DIFFRACTION	f_angle_d	1.044	3164
X-RAY DIFFRACTION	f_dihedral_angle_d	6.221	1858
X-RAY DIFFRACTION	f_chiral_restr	0.056	346
X-RAY DIFFRACTION	f_plane_restr	0.008	422

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 (%)
1.5008-1.5383	0.1791	146	0.1525	2879	X-RAY DIFFRACTION	94
1.5383-1.5799	0.1621	139	0.1453	2964	X-RAY DIFFRACTION	96
1.5799-1.6264	0.1738	155	0.1343	2880	X-RAY DIFFRACTION	96
1.6264-1.6789	0.1706	142	0.1381	2923	X-RAY DIFFRACTION	95
1.6789-1.7389	0.1777	148	0.1371	2933	X-RAY DIFFRACTION	95
1.7389-1.8085	0.1713	148	0.1392	2902	X-RAY DIFFRACTION	95
1.8085-1.8908	0.1752	135	0.1346	2919	X-RAY DIFFRACTION	95
1.8908-1.9904	0.1584	149	0.1312	2915	X-RAY DIFFRACTION	94
1.9904-2.1151	0.1532	145	0.128	2877	X-RAY DIFFRACTION	94
2.1151-2.2784	0.1368	146	0.1275	2884	X-RAY DIFFRACTION	93
2.2784-2.5075	0.1591	146	0.1325	2871	X-RAY DIFFRACTION	92
2.5075-2.8702	0.1534	146	0.1427	2847	X-RAY DIFFRACTION	91
2.8702-3.6152	0.1662	139	0.1462	2799	X-RAY DIFFRACTION	89
3.6152-30.3482	0.1708	131	0.1594	2630	X-RAY DIFFRACTION	80

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	2.4492	1.0702	-3.0329	0.4708	-1.304	3.8185	-0.2213	0.0962	0.4548	0.1148	-0.05	-0.1143	0.1979	0.2343	0.132	0.3149	0.0578	0.032	0.2761	-0.0354	0.2732	-17.4927	5.3533	21.6504
2	4.8958	0.5528	-0.54	1.4416	0.4381	1.4943	0.0776	0.1316	0.2928	0.0257	-0.0764	0.0943	-0.1123	-0.1593	-0.0173	0.1255	0.0026	0.0157	0.1052	-0.0283	0.122	-5.2036	-1.0707	15.5817
3	2.388	-0.6759	0.8343	0.6357	1.1749	6.9503	-0.0163	0.3332	0.2717	-0.4484	0.2962	-0.1384	-0.7254	0.5655	-0.1487	0.1984	-0.0622	0.0412	0.1658	-0.0004	0.1793	7.4595	-1.3762	-0.4596
4	0.9999	-0.0619	0.2543	1.2859	0.295	1.3447	-0.0212	0.0367	0.0186	0.0509	0.0065	0.016	0.1442	-0.0282	-0.0138	0.0618	-0.0003	-0.0049	0.0713	-0.0033	0.0685	-3.7599	-14.931	6.9364
5	0.5321	0.2591	0.2184	1.1007	0.1002	1.4368	0.029	-0.0271	0.1106	0.0583	-0.063	0.0682	-0.1941	-0.1086	0.031	0.0973	0.0208	0.0074	0.0862	-0.0116	0.1027	-9.0952	-8.0148	6.8885
6	1.4647	0.3766	-0.4579	1.4005	0.3623	1.4651	0.1233	-0.1946	-0.5395	0.1108	0.0433	0.5527	0.5015	-0.2575	-0.0311	0.2107	-0.0417	-0.0354	0.1319	0.0282	0.231	-9.0795	-33.5908	8.7809
7	1.1513	-0.7401	-0.7307	3.7398	2.2341	2.6069	0.014	0.1201	-0.2312	0.3064	-0.3432	0.6161	0.3728	-0.3308	0.2688	0.1571	-0.0375	0.0166	0.1276	-0.0256	0.1849	-11.2725	-31.6384	6.0471
8	0.6989	0.4342	-0.068	0.2315	-0.0679	0.2111	0.0231	0.0749	0.0785	-0.003	0.0462	-0.0035	0.009	0.0842	-0.0569	0.0771	0.0025	0.0144	0.0965	-0.0064	0.1003	1.6272	-10.9	4.5112
9	1.1844	0.344	-0.3141	1.3188	0.0719	1.5725	0.0366	-0.1882	0.0471	0.2111	-0.0338	0.0238	0.1202	0.1032	-0.0227	0.1236	0.0005	0.0055	0.1194	-0.0174	0.0979	-1.0496	-13.4545	17.4171
10	3.0766	-0.7931	-0.0244	1.2857	0.4968	1.1394	-0.0202	0.3662	0.0433	-0.2159	-0.0276	-0.0514	0.035	0.1382	0.0013	0.1006	0.0081	0.0104	0.137	0.0031	0.1083	0.8609	-14.7309	-7.4146
11	6.2821	-0.3507	-0.8408	1.713	0.8111	3.8569	0.1553	0.2395	-0.8104	-0.0928	-0.1006	0.277	0.6956	-0.3223	-0.1032	0.243	0.0035	-0.0563	0.1763	-0.0889	0.246	-11.1151	-39.3605	-11.9339
12	2.3098	-1.633	2.197	4.8519	0.1746	3.7793	-0.0232	0.1767	-0.0484	0.0889	0.0252	-0.455	0.1706	0.4399	0.0515	0.1952	0.069	-0.0307	0.2816	-0.09	0.2107	2.2689	-38.3628	-12.317
13	4.3399	0.9071	-1.5201	1.2127	1.1587	2.8304	-0.1089	0.177	-0.8723	-0.2983	0.1265	-0.2684	1.0593	0.5512	-0.0547	0.2799	0.1079	-0.0082	0.1976	-0.057	0.2273	9.2892	-38.39	-3.1007
14	0.3994	0.017	-0.2875	1.001	-0.1986	0.5415	-0.0297	0.0346	-0.0228	0.0264	-0.0216	-0.0349	0.0029	0.0486	0.0814	0.09	0.0122	-0.0011	0.1062	-0.0004	0.09	0.26	-26.8149	0.0504
15	0.7632	0.1102	0.0526	0.8884	0.4305	0.9377	0.0635	0.1133	-0.1597	0.003	-0.0252	0.0931	0.1481	-0.0198	-0.0035	0.1171	0.0163	-0.0196	0.0942	-0.0192	0.1209	-8.1119	-31.4748	-3.965
16	1.8866	0.6104	-0.4686	3.6588	-1.6223	3.1593	0.1206	0.3131	0.2611	-0.2485	0.126	0.2186	-0.1527	-0.004	-0.1285	0.1269	0.0165	0.0114	0.1164	0.0349	0.1083	-8.0127	-6.3554	-7.302
17	2.6142	0.3048	0.3015	2.1438	1.2347	2.382	0.1736	0.1145	0.1384	-0.0029	-0.1144	0.1818	-0.1623	-0.2336	0.0164	0.0984	0.0318	0.0029	0.1195	0.0234	0.1288	-11.5256	-5.8554	-3.7695
18	0.9534	-0.4299	0.3035	0.854	-0.2995	0.5864	0.0127	0.158	-0.0753	-0.0527	-0.0227	-0.0143	0.0284	0.0887	-0.0116	0.0928	0.0155	-0.0043	0.11	-0.0124	0.0933	1.3118	-27.5342	-5.4867
19	2.0546	-0.1404	1.3876	0.8281	0.0678	2.0917	0.0587	0.5317	-0.1195	-0.2811	0.0035	-0.0103	-0.0262	0.1275	-0.0185	0.1808	0.0358	-0.0185	0.2556	-0.0201	0.0992	-3.7767	-24.5705	-15.4089
20	2.9234	1.457	-0.1246	2.1567	-0.0335	1.4556	0.0842	-0.199	0.1293	0.0959	-0.0479	-0.0071	0.1444	0.1317	0.0259	0.1266	0.0198	-0.0212	0.0894	-0.0113	0.107	2.7078	-23.7993	8.9923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 468:474)
2	X-RAY DIFFRACTION	2	(chain A and resid 475:492)
3	X-RAY DIFFRACTION	3	(chain A and resid 493:501)
4	X-RAY DIFFRACTION	4	(chain A and resid 502:516)
5	X-RAY DIFFRACTION	5	(chain A and resid 517:537)
6	X-RAY DIFFRACTION	6	(chain A and resid 538:549)
7	X-RAY DIFFRACTION	7	(chain A and resid 550:560)
8	X-RAY DIFFRACTION	8	(chain A and resid 561:576)
9	X-RAY DIFFRACTION	9	(chain A and resid 577:599)
10	X-RAY DIFFRACTION	10	(chain A and resid 600:607)
11	X-RAY DIFFRACTION	11	(chain B and resid 474:483)
12	X-RAY DIFFRACTION	12	(chain B and resid 484:491)
13	X-RAY DIFFRACTION	13	(chain B and resid 492:497)
14	X-RAY DIFFRACTION	14	(chain B and resid 498:514)
15	X-RAY DIFFRACTION	15	(chain B and resid 515:537)
16	X-RAY DIFFRACTION	16	(chain B and resid 538:548)
17	X-RAY DIFFRACTION	17	(chain B and resid 549:558)
18	X-RAY DIFFRACTION	18	(chain B and resid 559:582)
19	X-RAY DIFFRACTION	19	(chain B and resid 583:598)
20	X-RAY DIFFRACTION	20	(chain B and resid 599:607)

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