PDB-2qvj: Crystal structure of a vesicular stomatitis virus nucleocapsid pr...

ID or keywords:

Entry

Database: PDB / ID: 2qvj

Title

Crystal structure of a vesicular stomatitis virus nucleocapsid protein Ser290Trp mutant

Components

Nucleocapsid protein

Keywords

RNA BINDING PROTEIN / nucleocapsid / Cytoplasm / Ribonucleoprotein / RNA-binding / Viral nucleoprotein / Virion

Function / homology

Function and homology information

RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function

Biological species

Vesicular stomatitis Indiana virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.8 Å

Authors

Luo, M. / Green, T.J. / Zhang, X. / Tsao, J. / Qiu, S.

Citation

Journal: J.Virol. / Year: 2008
Title: Role of intermolecular interactions of vesicular stomatitis virus nucleoprotein in RNA encapsidation.
Authors: Zhang, X. / Green, T.J. / Tsao, J. / Qiu, S. / Luo, M.

History

Deposition	Aug 8, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 8, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2qvj.cif.gz	781.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2qvj.ent.gz	662 KB	Display	PDB format
PDBx/mmJSON format	2qvj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2qvj_validation.pdf.gz	465 KB	Display	wwPDB validaton report
Full document	2qvj_full_validation.pdf.gz	498.7 KB	Display
Data in XML	2qvj_validation.xml.gz	69 KB	Display
Data in CIF	2qvj_validation.cif.gz	93.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvj ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvj	HTTPS FTP

-
Related structure data

Similar structure data	3pto-1 3pu0-1 3pmk-1 3pu4-1 2gic-1 3pu1-1 3ptx-1 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	#62 - Feb 2005 Major Histocompatibility Complex similarity (5)

Deposited unit

A: Nucleocapsid protein

B: Nucleocapsid protein

C: Nucleocapsid protein

D: Nucleocapsid protein

E: Nucleocapsid protein

237 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nucleocapsid protein

B: Nucleocapsid protein

C: Nucleocapsid protein

D: Nucleocapsid protein

E: Nucleocapsid protein

A: Nucleocapsid protein

B: Nucleocapsid protein

C: Nucleocapsid protein

D: Nucleocapsid protein

E: Nucleocapsid protein

defined by author&software
474 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	166.456, 236.652, 74.718
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

The biological assembly is a decamer consisting of the five copies of the N protein in the asymmetric unit plus an additional five copies created by rotation of the contents of the asymmetric unit by 180 degrees around the c-axis.

#1: Protein	Nucleocapsid protein / Protein N / Nucleoprotein / NP Mass: 47431.883 Da / Num. of mol.: 5 / Mutation: S290W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vesicular stomatitis Indiana virus / Genus: Vesiculovirus / Strain: Indiana / Gene: N / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03521, UniProt: A6H4P1*PLUS

#1: Protein

Nucleocapsid protein / Protein N / Nucleoprotein / NP

Mass: 47431.883 Da / Num. of mol.: 5 / Mutation: S290W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vesicular stomatitis Indiana virus / Genus: Vesiculovirus / Strain: Indiana / Gene: N / Plasmid: pET16b / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03521, UniProt: A6H4P1*PLUS

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5.5 % PEG 3350, 200 mM sodium chloride, 100mM sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 293.0K

-
Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→41.62 Å / Num. obs: 54826 / % possible obs: 74.3 % / Redundancy: 4.62 % / R_merge(I) obs: 0.084 / Net I/σ(I): 19
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.172 / Num. unique all: 3262 / % possible all: 44.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
PDB_EXTRACT	3	data extraction
SERGUI		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Resolution: 2.8→41.62 Å / Cor.coef. F_o:F_c: 0.878 / Cor.coef. F_o:F_c free: 0.839 / SU B: 35.983 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.286	2796	5.1 %	RANDOM
R_work	0.243	-	-	-
obs	0.246	54826	74.41 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.198 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.59 Å²	0 Å²	0 Å²
2-	-	-1.74 Å²	0 Å²
3-	-	-	-2.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→41.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16675	0	0	0	16675

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	17065
X-RAY DIFFRACTION	r_angle_refined_deg	0.953	1.963	23120
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.475	5	2100
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.78	24.052	765
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.887	15	2945
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.559	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	2510
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	12945
X-RAY DIFFRACTION	r_nbd_refined	0.182	0.2	7536
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	11889
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.119	0.2	363
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.127	0.2	155
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.102	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	1.126	1.5	10729
X-RAY DIFFRACTION	r_mcangle_it	2.03	2	16900
X-RAY DIFFRACTION	r_scbond_it	0.879	3	7294
X-RAY DIFFRACTION	r_scangle_it	1.379	4.5	6220

LS refinement shell

Resolution: 2.8→2.872 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	133	-
R_work	0.277	2172	-
all	-	2305	-
obs	-	-	42.79 %

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	0.0012	-0.0036	-0.0218	0.0969	0.0235	0.4344	0.1411	-0.015	-0.051	-0.0625	-0.0052	0.0932	-0.1083	0.0935	-0.1359	0.109	-0.0743	0.0423	0.0231	-0.0189	0.0039	37.8371	46.5418	20.7444
2	11.3192	-6.3224	-1.8597	3.6738	1.6889	3.2732	0.3748	0.0792	0.1653	0.7477	-0.1944	0.0949	-0.0173	0.5199	-0.1804	0.161	-0.0416	-0.0236	-0.0848	0.0146	-0.0599	52.102	35.6438	38.3204
3	0.4462	0.0465	-0.2923	0.0198	0.2487	5.3955	-0.0118	0.1007	0.0001	0.1062	0.0131	0.0697	0.1376	0.2099	-0.0014	0.2327	-0.0046	-0.0033	-0.1057	0.0087	0.0061	57.677	37.22	32.1757
4	0.1458	-0.7533	-0.6336	3.8912	3.2728	2.7526	-0.0718	0.1202	0.6465	-0.1568	-0.3621	0.1165	1.9191	-0.5703	0.4339	0.3561	-0.2474	0.0749	0.0395	0.0288	0.0028	43.1735	26.7949	31.9919
5	9.5532	-0.5757	5.6006	5.0369	4.6141	8.1847	-0.396	-0.028	-0.3935	0.5554	0.0699	0.9581	0.9762	-0.7689	0.3261	0.1805	-0.2409	0.1958	0.0928	0.0484	0.0384	39.7433	19.7787	35.013
6	0.146	0.2163	0.2157	0.3511	0.214	0.6836	0.0385	-0.0007	-0.0974	0.0423	0.0205	0.032	-0.0296	0.0405	-0.059	-0.0067	0.027	0.0146	0.0429	-0.0173	0.0002	41.3392	31.5873	9.6092
7	2.4016	-2.0856	-0.7599	3.1697	2.2539	2.1107	0.059	0.5819	0.0593	-0.5989	-0.2962	0.0114	-0.1274	-0.2122	0.2372	0.0297	-0.159	0.026	0.1036	0.1327	0.0258	43.9111	13.9972	-19.8498
8	1.0231	0.3886	-1.7346	3.3875	-1.6497	3.244	-0.0811	0.1423	-0.1285	-0.0438	0.0921	0.2048	0.1595	-0.181	-0.011	-0.1957	-0.0355	-0.0623	0.0561	0.0089	0.0319	24.8039	22.516	-5.2468
9	1.0045	-0.1235	1.1905	0.1331	-0.4134	2.0156	0.0206	-0.0541	0.0325	-0.0277	-0.0622	0.0213	-0.0138	0.0438	0.0416	0.107	0.1058	0.1113	0.0225	-0.0659	-0.0612	3.0123	59.6322	20.7106
10	4.0139	0.9263	-1.5244	1.8554	0.6377	1.7979	0.1445	-0.2007	-0.1989	0.0597	-0.0271	-0.1723	-0.0741	0.3647	-0.1173	-0.0818	-0.0297	0.0049	-0.0193	-0.0244	-0.0441	26.2155	64.2164	28.0352
11	0.2424	-0.636	-0.156	2.1166	0.2668	4.8695	-0.0061	-0.0088	-0.0065	0.1991	-0.1405	0.0555	0.4297	0.0343	0.1466	-0.1565	-0.0003	0.114	0.0164	0.0284	0.0094	18.8558	54.048	37.67
12	0.6628	-1.5554	-0.2789	13.8779	2.7563	4.1456	-0.1314	-0.4497	-0.7716	0.8699	0.0991	0.4298	1.8111	-0.0214	0.0322	0.1678	-0.0374	0.094	0.0199	0.0168	-0.0754	20.8863	38.7777	35.2509
13	0.3512	0.4117	0.9872	1.1702	1.4396	2.891	-0.0545	0.0848	-0.054	0.1263	-0.0176	0.0583	0.3639	-0.0521	0.0721	-0.0707	0.0127	0.031	0.0648	-0.0053	0.0168	20.065	52.5869	23.0262
14	0.4616	0.4565	0.425	1.339	0.5949	0.8188	0.0421	0.0071	-0.0528	-0.0709	-0.0835	-0.0117	-0.2956	-0.1641	0.0414	-0.0757	0.0517	-0.0371	0.0865	0.0147	-0.0491	12.245	52.8438	5.2681
15	2.3322	-0.897	-0.8501	0.3481	0.298	0.5747	-0.0142	-0.0442	-0.0752	-0.088	-0.1141	-0.0119	-0.1338	-0.0526	0.1283	-0.0669	-0.0085	-0.0422	0.0694	-0.0054	-0.0229	16.6825	37.8763	-4.2608
16	2.5415	0.7042	0.1667	2.2265	-1.7552	1.6084	0.0927	0.3008	-0.3677	-0.5127	-0.0642	0.1221	0.2227	0.1851	-0.0285	0.0376	0.0195	-0.0327	0.0059	-0.0402	0.0137	9.7486	33.6843	-9.4229
17	0.0777	-0.1711	-0.0337	0.4376	-0.0969	0.4929	-0.0498	0.0092	0.1085	-0.0832	-0.1161	0.0117	-0.0275	-0.0083	0.1659	-0.0117	0.0017	0.0282	0.034	0.0141	-0.0213	-32.5899	50.2347	20.9104
18	0.1417	-0.3483	-0.3646	0.8559	0.8959	0.9379	0.1361	-0.1109	-0.0612	0.0845	0.1848	-0.0396	-0.5148	0.0051	-0.3209	-0.0362	-0.0817	0.0135	0.1881	0.0754	-0.027	-16.275	68.0134	27.7399
19	0.6585	-0.7903	-0.9889	2.8683	1.5193	3.4066	-0.1171	0.0384	-0.3855	-0.1344	0.0703	0.1989	0.0684	0.3698	0.0468	-0.0663	0.032	0.0092	-0.0115	0.0381	-0.0267	-15.9166	54.9828	38.9164
20	4.3493	4.2863	3.5723	15.0491	10.5159	12.1963	0.2732	-0.56	-0.8396	-0.3612	-0.1285	-0.3933	0.8724	0.1474	-0.1447	0.0728	0.2701	-0.0044	0.0848	0.1024	-0.0636	-6.5965	43.343	34.6781
21	0.0083	0.0712	0.1215	0.6076	1.0373	1.7709	-0.0127	-0.0563	-0.0872	-0.2098	0.2006	0.0237	0.3046	0.3436	-0.1878	-0.0059	0.0474	0.0252	0.1311	0.0122	-0.0472	-14.1584	54.0551	21.8417
22	0.1243	-0.5583	-0.325	2.5072	1.4596	0.8498	0.1127	0.0035	0.0439	0.0206	-0.0452	-0.0241	0.0637	-0.0263	-0.0674	0.0045	-0.0016	-0.0186	0.0434	0.0163	-0.03	-20.2238	45.5103	3.9526
23	8.3118	1.6768	0.443	0.3439	0.075	0.0606	0.1516	1.095	0.105	-0.0633	-0.0294	0.1059	0.3557	0.1416	-0.1222	0.1935	-0.011	-0.0558	0.2121	-0.0372	-0.0938	-0.7122	45.0443	-18.0416
24	1.329	0.8826	-0.2897	0.5864	-0.2205	2.5317	-0.0956	0.1334	-0.1658	-0.1268	-0.0799	-0.1668	0.4143	-0.1961	0.1755	-0.0362	0.0412	-0.0152	-0.0046	-0.035	0.0323	-13.9656	29.5299	-4.9121
25	0.7475	1.0574	0.4939	1.5164	0.6777	0.3479	-0.076	0.1679	0.2665	-0.0272	0.1574	0.2204	0.2599	0.144	-0.0814	0.0407	0.0133	-0.0327	0.1287	0.0189	-0.1528	-61.0065	16.081	9.5373
26	0.6848	-0.3664	0.5628	0.2987	-0.2433	2.5503	0.0495	-0.2042	0.1854	0.1395	-0.0201	-0.0631	-0.2364	-0.294	-0.0294	-0.0227	0.0043	-0.0362	-0.0004	-0.0264	-0.0032	-49.5211	41.1696	34.5801
27	0.8241	-1.3238	0.7956	4.2777	-0.1238	3.9322	0.1623	-0.0039	0.0204	0.1866	-0.0726	0.1777	-0.0133	0.3273	-0.0897	-0.0898	-0.0007	-0.0314	-0.0552	-0.0485	-0.0278	-45.8345	35.5589	37.6063
28	8.9104	4.283	-1.956	3.5969	-1.6629	7.8649	0.1593	-0.4576	-0.5488	-0.0072	-0.6647	-0.0339	0.1462	2.1733	0.5054	0.0306	0.1197	-0.1548	0.2457	0.0623	-0.1291	-30.546	30.522	34.8815
29	0.1619	0.2153	0.0152	0.7221	0.8663	1.6444	0.1109	0.0466	0.1112	0.0603	0.0526	-0.0249	0.1871	0.0952	-0.1635	0.0214	0.0325	-0.0378	0.0579	0.0093	-0.0182	-45.1499	33.3261	14.1628
30	0.0164	0.0744	0.0956	0.3374	0.4336	0.5572	-0.1859	-0.0242	0.1291	0.0549	0.1033	-0.0141	0.0929	-0.0544	0.0825	-0.0137	0.0161	-0.0093	0.076	0.0247	-0.0302	-38.4124	24.2437	3.2959
31	5.0964	9.8155	-1.7699	18.9212	-3.2166	2.8137	-0.6479	0.2625	0.3057	-0.9355	1.0799	0.2654	1.1285	0.3866	-0.432	0.0982	0.161	-0.0686	0.0189	-0.0135	0.0723	-27.3693	34.7759	-21.4127
32	2.3996	-0.807	2.2023	3.4452	-1.5082	4.5752	0.157	0.2784	-0.2405	-0.2218	0.0197	-0.2558	0.2604	0.3907	-0.1767	-0.0596	0.0212	0.0242	-0.0484	-0.0566	0.0191	-29.3553	16.0629	-5.0016
33	0.4585	-0.9496	0.9079	2.1774	-1.9781	1.8431	-0.1444	0.2457	-0.0034	0.4887	-0.1639	-0.0127	-0.4423	0.1816	0.3084	-0.0039	-0.0177	-0.0676	0.0848	-0.0333	-0.0177	59.153	22.4247	10.112
34	0.8128	-0.8598	-0.2051	1.1233	0.9814	2.7853	0.0539	-0.1309	0.0402	0.1168	-0.1849	-0.0978	0.7043	0.0542	0.131	0.2443	-0.0434	-0.0224	0.0237	-0.0711	-0.0054	61.0548	-2.5167	41.8577
35	1.2469	-0.2574	-2.0597	1.4635	-0.5181	4.0331	-0.0011	0.2642	0.2539	0.4833	-0.0622	-0.2302	0.416	0.0932	0.0633	0.0333	-0.0181	-0.0565	0.0169	-0.0638	-0.0558	64.8593	-3.5844	32.8749
36	2.6763	3.7816	-0.3149	5.3487	-0.5806	3.4323	0.1823	0.1692	0.787	0.6562	-0.0225	0.4668	0.1512	-0.8599	-0.1599	0.063	-0.1004	0.0777	0.2513	-0.2736	0.0424	46.0879	-3.4303	34.2135
37	0.5552	-0.1347	1.2167	0.1953	-0.3032	2.6666	-0.0115	-0.0612	0.1125	-0.0047	0.0124	-0.0787	0.249	-0.1215	-0.001	-0.0033	0.004	0.0253	0.049	-0.0494	-0.0415	57.8909	-0.3395	12.4563
38	2.339	1.6916	1.0149	5.7144	-0.0997	0.5951	0.0841	-0.2375	-0.1494	-0.0948	-0.0409	0.1649	-0.3679	-0.0069	-0.0431	-0.1019	-0.017	0.0166	0.0075	-0.0122	-0.0609	42.2931	5.029	1.8584
39	8.8572	-12.2796	-0.4934	18.0979	-1.5403	4.6374	0.5887	0.5701	0.1309	-1.4227	-0.5183	0.0843	0.4661	-0.9377	-0.0704	-0.0177	-0.0922	0.0058	0.215	0.0689	-0.1372	43.8781	-15.693	-19.3799
40	1.0067	0.8949	-0.1243	2.5127	0.6748	1.0735	-0.0371	0.0717	0.2967	-0.3381	0.069	0.5044	0.2343	0.1358	-0.0319	-0.115	0.0623	-0.0521	0.0206	0.0414	0.0046	34.2893	3.6602	-5.5323

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 64	1 - 63
2	X-RAY DIFFRACTION	2	A	A	65 - 80	64 - 79
3	X-RAY DIFFRACTION	3	A	A	81 - 132	80 - 131
4	X-RAY DIFFRACTION	4	A	A	133 - 148	132 - 147
5	X-RAY DIFFRACTION	5	A	A	149 - 180	148 - 179
6	X-RAY DIFFRACTION	6	A	A	181 - 346	180 - 345
7	X-RAY DIFFRACTION	7	A	A	347 - 374	346 - 373
8	X-RAY DIFFRACTION	8	A	A	375 - 422	374 - 421
9	X-RAY DIFFRACTION	9	B	B	2 - 64	1 - 63
10	X-RAY DIFFRACTION	10	B	B	65 - 103	64 - 102
11	X-RAY DIFFRACTION	11	B	B	104 - 149	103 - 148
12	X-RAY DIFFRACTION	12	B	B	150 - 179	149 - 178
13	X-RAY DIFFRACTION	13	B	B	180 - 235	179 - 234
14	X-RAY DIFFRACTION	14	B	B	236 - 306	235 - 305
15	X-RAY DIFFRACTION	15	B	B	307 - 355	306 - 354
16	X-RAY DIFFRACTION	16	B	B	356 - 422	355 - 421
17	X-RAY DIFFRACTION	17	C	C	2 - 65	1 - 64
18	X-RAY DIFFRACTION	18	C	C	66 - 106	65 - 105
19	X-RAY DIFFRACTION	19	C	C	107 - 147	106 - 146
20	X-RAY DIFFRACTION	20	C	C	148 - 179	147 - 178
21	X-RAY DIFFRACTION	21	C	C	180 - 238	179 - 237
22	X-RAY DIFFRACTION	22	C	C	239 - 338	238 - 337
23	X-RAY DIFFRACTION	23	C	C	339 - 376	338 - 375
24	X-RAY DIFFRACTION	24	C	C	377 - 422	376 - 421
25	X-RAY DIFFRACTION	25	D	D	2 - 44	1 - 43
26	X-RAY DIFFRACTION	26	D	D	45 - 101	44 - 100
27	X-RAY DIFFRACTION	27	D	D	102 - 148	101 - 147
28	X-RAY DIFFRACTION	28	D	D	149 - 179	148 - 178
29	X-RAY DIFFRACTION	29	D	D	180 - 276	179 - 275
30	X-RAY DIFFRACTION	30	D	D	277 - 349	276 - 348
31	X-RAY DIFFRACTION	31	D	D	350 - 374	349 - 373
32	X-RAY DIFFRACTION	32	D	D	375 - 422	374 - 421
33	X-RAY DIFFRACTION	33	E	E	2 - 45	1 - 44
34	X-RAY DIFFRACTION	34	E	E	46 - 83	45 - 82
35	X-RAY DIFFRACTION	35	E	E	84 - 145	83 - 144
36	X-RAY DIFFRACTION	36	E	E	146 - 190	145 - 189
37	X-RAY DIFFRACTION	37	E	E	191 - 288	190 - 287
38	X-RAY DIFFRACTION	38	E	E	289 - 342	288 - 341
39	X-RAY DIFFRACTION	39	E	E	343 - 372	342 - 371
40	X-RAY DIFFRACTION	40	E	E	373 - 422	372 - 421

-
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://pdbjlvh1.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