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

ID or keywords:

Entry

Database: PDB / ID: 6npm

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 / symbiont-mediated suppression of host antigen processing and presentation / 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 / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response ...
Similarity search - Function

Biological species

Epstein-Barr virus (Epstein-Barr virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.603 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	6npm.cif.gz	179.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6npm.ent.gz	144.1 KB	Display	PDB format
PDBx/mmJSON format	6npm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6npm_validation.pdf.gz	450 KB	Display	wwPDB validaton report
Full document	6npm_full_validation.pdf.gz	450.6 KB	Display
Data in XML	6npm_validation.xml.gz	17.7 KB	Display
Data in CIF	6npm_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/6npm ftp://data.pdbj.org/pub/pdb/validation_reports/np/6npm	HTTPS FTP

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Related structure data

Related structure data	6npiC 6nppC 1vhiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6npp-d 2e9v-1 4ygd-1 4ygc-1 2ywp-d 5opv-d 3jvr-d 6npi-d 5svv-2 6vh6-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

30.8 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)	59.458, 67.951, 69.546
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-KVD / 5-(phenylethynyl)pyridine-3-carboxylic acid Mass: 223.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₉NO₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 447 / 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: 46.4 % / Description: Rectangular rods
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50 mM MES pH 6.5, 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 PILATUS3 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: 1.6→30.955 Å / Num. obs: 37306 / % possible obs: 99 % / Redundancy: 5.3 % / B_iso Wilson estimate: 13.44 Å² / Net I/σ(I): 41.7
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2574 / % possible all: 97

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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: 1.603→30.955 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.99

	R_factor	Num. reflection	% reflection
R_free	0.1696	2003	5.37 %
R_work	0.1432	-	-
obs	0.1446	37305	99.12 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 18.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.603→30.955 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2101	0	17	447	2565

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2238
X-RAY DIFFRACTION	f_angle_d	1.02	3051
X-RAY DIFFRACTION	f_dihedral_angle_d	3.37	1831
X-RAY DIFFRACTION	f_chiral_restr	0.058	341
X-RAY DIFFRACTION	f_plane_restr	0.008	403

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 (%)
1.6033-1.6434	0.1772	142	0.1476	2432	X-RAY DIFFRACTION	97
1.6434-1.6879	0.1816	142	0.1439	2496	X-RAY DIFFRACTION	100
1.6879-1.7375	0.1833	145	0.1436	2518	X-RAY DIFFRACTION	100
1.7375-1.7936	0.1667	135	0.1437	2512	X-RAY DIFFRACTION	100
1.7936-1.8577	0.1834	150	0.1469	2498	X-RAY DIFFRACTION	100
1.8577-1.9321	0.1861	139	0.1547	2523	X-RAY DIFFRACTION	99
1.9321-2.02	0.1683	142	0.1425	2499	X-RAY DIFFRACTION	100
2.02-2.1265	0.17	139	0.1362	2551	X-RAY DIFFRACTION	100
2.1265-2.2596	0.1682	144	0.1381	2510	X-RAY DIFFRACTION	100
2.2596-2.434	0.1763	145	0.1334	2536	X-RAY DIFFRACTION	100
2.434-2.6789	0.1508	149	0.1373	2542	X-RAY DIFFRACTION	100
2.6789-3.0662	0.1706	141	0.1419	2554	X-RAY DIFFRACTION	99
3.0662-3.8619	0.1701	144	0.1416	2547	X-RAY DIFFRACTION	98
3.8619-30.961	0.1631	146	0.1534	2584	X-RAY DIFFRACTION	95

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	3.0416	0.9559	-3.1989	0.3245	-1.0097	3.3646	-0.1476	-0.3553	0.3706	0.3768	0.0359	0.0602	0.2035	0.5743	0.2649	0.2717	0.0322	0.0038	0.2523	-0.04	0.2307	-17.3435	5.3738	21.7741
2	4.6941	0.3512	-0.5576	0.8066	0.0716	1.3229	0.066	-0.005	0.0665	-0.0107	-0.1402	0.0359	-0.1117	-0.037	-0.0164	0.1465	0.0039	-0.0001	0.1151	-0.0341	0.1331	-5.1492	-1.1375	15.526
3	2.0374	0.1157	0.7834	1.5913	2.0381	8.2244	0.0493	0.2569	0.2172	-0.3746	0.2057	-0.0279	-0.6959	0.4415	-0.3389	0.2287	-0.0433	0.0145	0.1629	0.0177	0.1787	7.0852	-1.4644	-1.0217
4	0.9563	0.0352	0.1581	0.872	0.108	1.0964	-0.0385	0.0043	-0.0211	-0.0217	0.0039	-0.0138	0.1327	0.0258	0.0117	0.101	0.002	-0.0132	0.0735	-0.0081	0.0975	-3.9665	-15.181	6.9927
5	0.6526	-0.0525	-0.0616	0.8751	0.0914	1.5539	0.0467	-0.0372	0.0549	0.0422	-0.0593	0.0274	-0.1529	-0.0803	-0.0249	0.1181	0.0075	0.0019	0.084	-0.0096	0.1083	-8.7419	-8.3156	6.6871
6	0.8766	0.2908	-0.38	2.5384	-0.4529	1.5153	0.0078	-0.0517	-0.2163	0.2563	0.1158	0.4334	0.2008	-0.2141	-0.0376	0.1672	-0.0236	-0.0075	0.1181	0.018	0.1845	-9.1634	-33.6369	8.9153
7	0.9008	-1.0359	-0.5677	3.7301	2.5678	2.7951	0.0311	-0.0308	-0.1212	0.1692	-0.2961	0.4845	0.2645	-0.2139	0.354	0.1315	-0.0252	0.0169	0.1133	0.0092	0.1757	-11.3528	-31.6346	6.2028
8	0.7028	0.3777	-0.0487	0.4312	-0.312	0.6069	0.0061	-0.0082	0.0459	0.0137	-0.0201	0.0141	-0.0093	0.0871	-0.0016	0.0998	-0.0007	0.0051	0.0859	-0.0073	0.1084	2.0084	-10.7085	4.5808
9	0.942	-0.0549	-0.6695	1.0213	0.0046	1.6277	0.0086	-0.1439	0.079	0.1341	0.0187	0.01	0.1155	0.1174	-0.0026	0.1234	0.0003	-0.0068	0.1199	-0.0135	0.1084	-1.3038	-13.6345	17.0876
10	3.6151	-1.044	-0.7769	1.3283	0.9315	1.0488	0.0314	0.4919	0.0261	-0.1553	-0.1286	-0.0498	0.0851	0.0654	0.0002	0.1351	-0.0057	0.0137	0.1587	0.0026	0.1306	0.8794	-14.8926	-7.4225
11	6.9069	-0.0679	-0.8054	2.2211	1.0484	3.6667	-0.0577	-0.0051	-0.6849	-0.1418	-0.2097	0.6123	0.4513	-0.4358	0.1433	0.1939	-0.0277	-0.024	0.1567	-0.0493	0.2631	-11.1015	-40.0008	-11.6982
12	1.8107	-0.1511	1.3188	4.2461	-1.2173	1.304	0.2293	0.1979	-0.285	0.0903	-0.0567	-0.3489	0.2139	0.7167	-0.2317	0.1918	0.0433	-0.0248	0.2419	-0.0551	0.1875	3.1242	-38.9763	-12.7769
13	3.9094	0.8069	-0.6648	1.7728	1.4304	5.649	0.0651	0.1572	-0.6504	-0.1775	0.1901	-0.2617	0.9895	0.4769	-0.296	0.2649	0.0727	-0.027	0.1979	-0.0389	0.2155	8.9413	-38.715	-2.8696
14	0.1142	-0.023	-0.1121	0.7511	-0.0737	0.7185	-0.0429	-0.039	0.0157	0.0589	-0.0078	-0.0137	-0.0656	0.0204	0.0451	0.1068	0.0032	0.0029	0.0951	0.0086	0.1128	0.269	-26.9681	-0.1491
15	0.4227	0.0151	0.1034	0.7638	0.2949	1.0236	0.0242	0.0157	-0.0847	0.0217	-0.0143	0.0517	0.1105	-0.0797	0.0138	0.1179	-0.0005	-0.0013	0.089	-0.0034	0.1358	-8.1576	-31.6314	-3.9611
16	1.8623	1.2147	-0.5989	4.476	-2.2771	3.0018	0.03	0.2746	0.2042	0.1985	0.2608	0.2077	-0.2262	-0.1398	-0.224	0.1368	0.0208	0.0119	0.1171	0.0387	0.1222	-8.5394	-6.8354	-7.218
17	2.83	1.3203	0.3399	2.7325	1.092	2.3789	0.1703	0.1457	0.1367	0.0282	-0.1191	0.0729	-0.1135	-0.2049	0.0336	0.1051	0.0376	0.0006	0.1258	0.0188	0.1405	-11.4809	-5.9912	-3.8438
18	0.4798	-0.2298	0.3408	0.6784	-0.4381	0.822	0.0002	0.1029	-0.0644	-0.0234	-0.0242	0.013	0.0003	0.0758	0.0239	0.1019	0.0059	-0.0007	0.0868	-0.0056	0.1133	1.3679	-27.7653	-5.4352
19	2.3968	0.1552	1.2485	1.5337	0.1091	2.0852	-0.0289	0.2799	-0.1136	-0.2239	0.0267	-0.0053	-0.2162	0.0807	0.0251	0.1465	0.022	-0.0023	0.1695	-0.0076	0.1149	-3.7312	-24.9301	-15.4169
20	4.4758	2.071	0.0302	2.3664	0.3535	1.2715	0.0128	-0.3028	0.1238	0.0333	-0.0806	-0.026	0.0319	0.071	0.0752	0.1367	0.024	-0.0078	0.1154	-0.0015	0.1158	2.6605	-23.9821	9.0078

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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