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

ID or keywords:

Entry

Database: PDB / ID: 6npp

Title

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

Components

EBNA1
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 / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / enzyme-substrate adaptor activity / endonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription ...
Similarity search - Function

Biological species

Epstein-Barr virus (Epstein-Barr virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.35 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 18, 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

-
Download

PDBx/mmCIF format	6npp.cif.gz	183.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6npp.ent.gz	146.2 KB	Display	PDB format
PDBx/mmJSON format	6npp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6npp_validation.pdf.gz	730.9 KB	Display	wwPDB validaton report
Full document	6npp_full_validation.pdf.gz	732.5 KB	Display
Data in XML	6npp_validation.xml.gz	18.1 KB	Display
Data in CIF	6npp_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/6npp ftp://data.pdbj.org/pub/pdb/validation_reports/np/6npp	HTTPS FTP

-
Related structure data

Related structure data	6npiC 6npmC 1vhiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6npm-d 6vh6-d 6sub-d 2f93-d 5svw-1 3l9e-1 5svv-2 1h2s-d 4zr0-1 3gqf-2 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

Deposited unit

A: Epstein-Barr nuclear antigen 1

B: EBNA1

hetero molecules

30.2 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 exists as a dimer in solution

Unit cell

Length a, b, c (Å)	59.353, 68.526, 69.897
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.: 1 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: Protein	EBNA1 Mass: 14650.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: GD1 / Gene: EBNA1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0J719, UniProt: P03211*PLUS
#3: Chemical	ChemComp-KWG / 3-(phenylethynyl)-2-(1H-pyrrol-1-yl)benzoic acid Mass: 287.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₃NO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.37 Å³/Da / Density % sol: 48.15 % / 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

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 1, 2018 / Details: Varimax
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.35→50 Å / Num. obs: 61748 / % possible obs: 97 % / Redundancy: 9.6 % / B_iso Wilson estimate: 15.28 Å² / R_sym value: 0.113 / Net I/σ(I): 16.5
Reflection shell	Resolution: 1.35→1.37 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2490 / R_sym value: 0.594 / % possible all: 80

-
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: 1.35→22.621 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.83

	R_factor	Num. reflection	% reflection
R_free	0.1845	2008	4.01 %
R_work	0.1578	-	-
obs	0.1588	50030	79.05 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→22.621 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2101	0	22	485	2608

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2265
X-RAY DIFFRACTION	f_angle_d	1.027	3090
X-RAY DIFFRACTION	f_dihedral_angle_d	3.187	1324
X-RAY DIFFRACTION	f_chiral_restr	0.071	341
X-RAY DIFFRACTION	f_plane_restr	0.008	410

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 (%)
1.3834-1.4208	0.2862	25	0.2455	578	X-RAY DIFFRACTION	14
1.4208-1.4626	0.2962	64	0.2199	1593	X-RAY DIFFRACTION	37
1.4626-1.5098	0.2041	123	0.2135	2927	X-RAY DIFFRACTION	69
1.5098-1.5637	0.2355	162	0.2019	3829	X-RAY DIFFRACTION	89
1.5637-1.6263	0.2263	175	0.1832	4119	X-RAY DIFFRACTION	96
1.6263-1.7003	0.2283	178	0.1813	4228	X-RAY DIFFRACTION	98
1.7003-1.7899	0.2116	182	0.1779	4270	X-RAY DIFFRACTION	99
1.7899-1.902	0.2336	173	0.1814	4285	X-RAY DIFFRACTION	99
1.902-2.0488	0.1872	181	0.1545	4322	X-RAY DIFFRACTION	100
2.0488-2.2548	0.1893	186	0.1485	4337	X-RAY DIFFRACTION	100
2.2548-2.5806	0.157	177	0.1487	4369	X-RAY DIFFRACTION	99
2.5806-3.2498	0.1607	181	0.1484	4397	X-RAY DIFFRACTION	100
3.2498-22.621	0.1733	192	0.1469	4581	X-RAY DIFFRACTION	100

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	2.7204	0.4095	-2.3942	0.9912	-0.9628	2.4977	-0.1704	-0.3575	-0.0027	0.3225	0.1216	0.2474	0.0703	0.4137	0.1512	0.2423	0.0023	0.0028	0.2352	-0.0521	0.1733	-17.3774	5.6825	21.5617
2	4.803	0.3693	-0.7483	0.8171	0.3517	1.2393	0.0853	0.248	0.186	-0.0109	-0.1375	0.0801	-0.2232	-0.1331	-0.0162	0.17	-0.0003	0.0068	0.1384	-0.0308	0.1453	-5.1799	-0.8891	15.325
3	1.1612	0.25	1.1882	1.1054	1.7529	7.077	-0.0015	0.2624	0.3258	-0.251	0.0894	0.0289	-0.6675	0.4818	-0.1234	0.2356	-0.0485	0.0273	0.1606	0.0181	0.1742	7.151	-1.563	-1.3149
4	0.4061	-0.1959	0.3282	0.6575	-0.1744	0.7465	-0.0446	-0.085	-0.0587	0.0008	-0.0581	0.003	0.116	0.0693	0.0894	0.139	-0.0143	-0.0009	0.0952	-0.0078	0.1115	-3.9688	-15.1399	7.0171
5	0.7062	0.2158	0.2985	1.1846	0.2395	1.383	0.0069	0	0.1291	-0.0508	-0.07	0.1135	-0.1672	-0.0974	0.0529	0.1652	0.0139	0.0018	0.1168	-0.02	0.1436	-8.7636	-8.29	6.5771
6	1.4397	0.2419	-0.3055	1.7719	0.0567	1.2488	0.0221	-0.2579	-0.1094	0.198	-0.0096	0.1752	0.2698	-0.1778	0.0046	0.2053	-0.0175	0.0022	0.1635	0.0285	0.1883	-9.218	-33.534	9.2761
7	0.9339	-0.5779	-0.357	3.7427	2.3814	2.601	0.0509	0.0183	-0.1359	0.202	-0.1789	0.3078	0.205	-0.1548	0.2665	0.1863	-0.0067	0.024	0.1419	0.0111	0.2028	-11.3711	-32.0276	6.468
8	0.5766	0.3443	-0.212	0.2196	-0.1919	0.2128	0.0316	-0.0172	-0.0221	0.0267	-0.0074	-0.0169	-0.0197	-0.0043	-0.0088	0.155	-0.0003	0.0031	0.1124	-0.0032	0.1307	1.6264	-11.1684	4.5914
9	1.48	1.312	-0.0492	1.431	0.1372	1.0261	0.0502	-0.3229	0.0871	0.2648	-0.1094	0.1525	0.1952	0.1557	0.0208	0.1759	-0.0052	0.0117	0.1361	-0.0142	0.13	-0.9953	-13.6076	16.5165
10	3.31	-1.4474	-0.013	0.9189	0.2307	0.1642	0.1118	0.3265	0.07	-0.1004	-0.0816	0.0324	-0.0787	0.026	0.0815	0.1724	0.0058	0.0011	0.1452	0.0098	0.1406	0.6379	-14.9366	-7.8704
11	5.7868	0.823	-1.074	1.5003	0.4236	3.0068	-0.0851	0.3751	-0.8681	-0.181	0.0334	0.5486	0.3283	-0.4691	0.1094	0.2081	-0.0053	-0.0106	0.1866	-0.0125	0.325	-11.4106	-39.9517	-11.0841
12	3.6553	0.8565	2.2258	6.0347	-1.8683	2.6136	0.3283	0.1898	-0.2315	0.2566	-0.0921	-0.4217	0.0523	0.7565	-0.3922	0.2358	0.0428	-0.019	0.2525	-0.0381	0.221	2.1723	-39.2636	-12.0031
13	3.8044	0.892	-1.2034	1.3462	1.8138	5.4583	-0.0088	0.19	-0.7453	-0.058	0.2251	-0.2159	1.059	0.4898	-0.153	0.2727	0.0683	-0.0246	0.2164	-0.0473	0.2644	8.8615	-38.8667	-2.423
14	0.4709	-0.158	-0.0302	0.8136	0.078	0.5065	-0.0154	-0.0332	-0.0448	0.0529	-0.0224	-0.0188	-0.0671	0.032	-0.0472	0.135	0.0027	0.0092	0.1119	0.0089	0.1243	0.2766	-27.1103	0.2836
15	0.5944	0.0905	0.4267	0.6792	0.3771	0.9831	0.0342	-0.0167	-0.1615	0.0098	-0.0023	0.0479	0.0986	-0.0242	-0.0243	0.1659	0.0111	0.0013	0.1228	0.0009	0.1458	-8.1386	-31.7614	-3.6001
16	3.0787	2.4563	-1.1516	5.9003	-3.4266	4.0285	0.1371	0.2177	0.2296	0.2314	0.0994	0.232	-0.0679	-0.0881	-0.2332	0.1504	0.0306	0.0241	0.1022	0.0176	0.1388	-8.4682	-7.265	-7.3761
17	2.6907	1.0979	0.418	1.7698	0.7067	1.8742	0.1437	0.1088	0.0977	0.1106	-0.0718	0.0478	-0.043	-0.0707	-0.0823	0.1459	0.0386	0.002	0.1204	0.0139	0.1532	-11.4746	-6.1812	-4.0802
18	0.8567	-0.0436	0.2911	0.4294	-0.1967	0.506	0.0367	0.0782	-0.074	-0.021	-0.0405	0.0013	0.0235	0.0326	-0.0056	0.1537	0.0153	-0.0018	0.1141	-0.0002	0.1396	1.6919	-27.9531	-5.3194
19	1.8966	0.0987	1.759	0.4837	0.2054	2.1449	0.0165	0.2613	-0.0902	-0.1272	0.0351	-0.0323	-0.076	0.1065	-0.081	0.1795	0.0153	0.0028	0.1791	-0.0043	0.1191	-3.4953	-25.0353	-15.4804
20	2.2142	0.9729	-0.1935	1.4082	-0.1832	1.0084	0.0944	-0.2206	0.1004	0.0443	-0.0827	0.0089	0.097	0.0361	-0.106	0.1776	0.0065	-0.0182	0.1135	-0.0069	0.1433	2.6653	-23.9342	9.2157

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)

-
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

-
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

-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

-
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