PDB-5vap: Crystal structure of eVP30 C-terminus and eNP peptide

ID or keywords:

Entry

Database: PDB / ID: 5vap

Title

Crystal structure of eVP30 C-terminus and eNP peptide

Components

Minor nucleoprotein VP30
NP

Keywords

VIRAL PROTEIN / function class / known biology activity

Function / homology

Function and homology information

viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm /

ribonucleoprotein complex /

RNA binding / zinc ion binding / identical protein binding
Similarity search - Function

Biological species

Ebola virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.85 Å

Authors

XU, W. / WU, C. / Leung, D.W. / Amarasinghe, G.K.

Funding support

United States, 9items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI107056	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI123926	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	P01AI120943	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI114654	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	U191099565	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	U19AI109945	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	U19AI109664	United States
Defense Threat Reduction Agency (DTRA)	HDTRA1-14-0013	United States
Defense Threat Reduction Agency (DTRA)	HDTRA1-12-1-0051	United States

Citation

Journal: Nat Commun / Year: 2017
Title: Ebola virus VP30 and nucleoprotein interactions modulate viral RNA synthesis.
Authors: Xu, W. / Luthra, P. / Wu, C. / Batra, J. / Leung, D.W. / Basler, C.F. / Amarasinghe, G.K.

History

Deposition	Mar 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 21, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5vap.cif.gz	119 KB	Display	PDBx/mmCIF format
PDB format	pdb5vap.ent.gz	95.3 KB	Display	PDB format
PDBx/mmJSON format	5vap.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/va/5vap ftp://data.pdbj.org/pub/pdb/validation_reports/va/5vap	HTTPS FTP

-
Related structure data

Related structure data	5vaoC C: citing same article (ref.)
Similar structure data	5cfi-4 3h96-4 5fmt-2 2n9u-d 3mcf-2 7a99-2 1h4o-2 1u27-d 1oc3-2 1m5t-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 (5)

Deposited unit

A: Minor nucleoprotein VP30

D: NP

B: Minor nucleoprotein VP30

C: NP

28.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Minor nucleoprotein VP30

D: NP

defined by author&software
14.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Minor nucleoprotein VP30

C: NP

defined by author&software
14.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.461, 55.078, 114.621
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 142 - 251 / Label seq-ID: 1 - 110

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	C

#1: Protein	Minor nucleoprotein VP30 / Transcription activator VP30 Mass: 12900.914 Da / Num. of mol.: 2 / Fragment: UNP residues 142-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus / Gene: VP30 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q77DJ5
#2: Protein/peptide	NP Mass: 1269.467 Da / Num. of mol.: 2 / Fragment: UNP residues 600-611 Source method: isolated from a genetically manipulated source Details: eNP 600-611 / Source: (gene. exp.) Ebola virus / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D5W865, UniProt: O72142*PLUS
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.7 Å³/Da / Density % sol: 54.42 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion / pH: 7 / Details: 0.2 M Potassium phosphate monobasic, 20%PEG3350

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9792601 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015

Radiation

Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792601 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 26341 / % possible obs: 99.6 % / Redundancy: 4.8 % / R_merge(I) obs: 0.058 / R_pim(I) all: 0.03 / R_rim(I) all: 0.066 / Χ²: 1.639 / Net I/σ(I): 11.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.85-1.88	4.8	0.636	0.804	0.309	0.71	0.909	100
1.88-1.92	4.8	0.531	0.867	0.257	0.591	1.074	100
1.92-1.95	4.8	0.402	0.899	0.197	0.449	0.917	99.9
1.95-1.99	4.8	0.305	0.945	0.149	0.341	0.97	100
1.99-2.04	4.8	0.27	0.949	0.132	0.302	1.06	100
2.04-2.08	4.9	0.244	0.967	0.117	0.271	1.428	99.8
2.08-2.14	4.8	0.18	0.97	0.089	0.202	1.262	99.8
2.14-2.19	4.8	0.153	0.982	0.075	0.171	1.233	99.9
2.19-2.26	4.8	0.177	0.985	0.084	0.196	1.847	99.9
2.26-2.33	4.8	0.113	0.989	0.055	0.126	1.386	100
2.33-2.41	4.8	0.096	0.991	0.047	0.107	1.438	99.9
2.41-2.51	4.8	0.085	0.992	0.042	0.095	1.453	99.8
2.51-2.63	4.8	0.072	0.994	0.035	0.08	1.541	99.9
2.63-2.76	4.8	0.064	0.996	0.032	0.072	1.702	99.9
2.76-2.94	4.8	0.059	0.996	0.029	0.066	1.79	99.8
2.94-3.16	4.8	0.057	0.996	0.028	0.063	2.243	99.9
3.16-3.48	4.7	0.057	0.995	0.029	0.064	3.123	100
3.48-3.99	4.7	0.049	0.996	0.025	0.055	3.314	99.7
3.99-5.02	4.5	0.039	0.997	0.02	0.044	2.474	99.7
5.02-50	4.3	0.033	0.997	0.017	0.037	1.646	95.4

-
Processing

Software

Name	Version	Classification
HKL-3000		data scaling
REFMAC	5.8.0158	refinement
PDB_EXTRACT	3.22	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Resolution: 1.85→50 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.928 / SU B: 6.16 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2325	1366	5.3 %	RANDOM
R_work	0.1939	-	-	-
obs	0.1959	24591	96.32 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 89.11 Å² / B_iso mean: 25.378 Å² / B_iso min: 10.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	-0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: final / Resolution: 1.85→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1973	0	0	119	2092
B_iso mean	-	-	-	29.74	-
Num. residues	-	-	-	-	246

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	2087
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2012
X-RAY DIFFRACTION	r_angle_refined_deg	1.351	1.969	2840
X-RAY DIFFRACTION	r_angle_other_deg	0.958	3	4662
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.815	5	260
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.335	23.034	89
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.828	15	383
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.056	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	333
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2276
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	427

Refine LS restraints NCS

Ens-ID: 1 / Number: 7294 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.85→1.898 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	70	-
R_work	0.247	1356	-
all	-	1426	-
obs	-	-	73.2 %

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	0.8091	1.8918	-0.5517	5.5933	-4.7833	10.8342	-0.0544	-0.0784	-0.1129	-0.171	-0.1632	-0.3132	0.3135	-0.0734	0.2175	0.1258	-0.0023	0.0384	0.0723	0.0122	0.0874	66.7921	-4.3143	144.0809
2	0.8619	-1.6124	-0.8099	3.1986	0.759	5.9903	-0.0891	0.0707	0.0179	0.1238	-0.1885	-0.1639	0.0902	0.5207	0.2776	0.0687	-0.0156	0.0287	0.1308	0.0211	0.1429	71.6633	0.9192	137.2722
3	1.7841	1.3354	2.1956	1.645	0.2032	5.9698	0.0114	0.0924	-0.1138	0.0459	0.0519	-0.1088	-0.122	0.1855	-0.0634	0.0774	-0.0115	0.01	0.0862	0.0064	0.0942	72.2365	6.7721	131.403
4	2.3968	1.6419	0.2267	6.8894	-2.1069	0.9116	0.0197	0.2488	0.0163	0.2541	-0.0974	-0.1729	-0.0891	0.1116	0.0777	0.0722	-0.0158	0.0253	0.1619	-0.0132	0.0405	66.2418	5.4347	123.0951
5	4.9632	-1.5788	1.8635	1.2469	-0.3651	0.7952	0.118	0.3009	-0.1754	0.0014	-0.0788	-0.0774	0.0497	0.0752	-0.0392	0.1052	-0.0025	0.0151	0.1148	-0.0722	0.1474	62.3168	0.1152	128.3566
6	0.3444	-0.2646	-0.3136	0.8016	2.2277	6.8913	0.0635	0.0226	-0.1491	0.0123	0.006	0.0552	0.1106	0.0408	-0.0695	0.12	-0.0071	0.0056	0.0833	-0.0001	0.0968	59.5355	1.2044	136.6458
7	1.2045	0.1125	3.2982	0.6269	0.4761	9.2968	-0.0213	-0.0872	-0.0804	0.1602	0.0824	-0.1251	-0.102	-0.1565	-0.0611	0.1736	0.0044	-0.0474	0.0507	0.0368	0.1887	58.7398	2.0009	143.9337
8	0.2906	0.9995	1.1238	6.6563	1.9958	5.7747	0.0493	-0.0755	0.0505	0.3926	-0.0894	0.1561	0.2482	-0.3138	0.0402	0.187	0.0164	-0.0163	0.1031	-0.0349	0.1042	55.3366	9.1206	149.3565
9	10.3191	5.1476	-0.5374	2.7786	-0.4806	0.2427	-0.1757	-0.1291	-0.0855	0.0824	0.0647	-0.1422	-0.1679	-0.1149	0.1111	0.1982	0.0667	-0.0616	0.1168	-0.0393	0.1084	59.1045	16.1593	145.4229
10	1.7824	-2.4628	-1.4632	8.6373	1.4463	1.2733	0.0163	-0.0506	0.0438	0.263	-0.0212	-0.2025	-0.0432	0.0345	0.0049	0.1151	-0.0266	-0.0224	0.0839	-0.0052	0.096	62.8694	19.058	139.7272
11	8.85	-4.7422	-2.1764	7.6579	-0.1213	0.8616	0.1219	0.1195	0.3612	0.1264	-0.0386	-0.1498	-0.0884	-0.0253	-0.0833	0.1301	-0.0386	-0.0272	0.0546	0.0025	0.119	58.1573	23.1026	136.2763
12	3.7379	3.1621	-2.3417	4.2091	-1.7098	1.5155	0.0194	-0.1603	0.042	-0.0263	-0.0045	0.0022	-0.0065	0.1213	-0.0149	0.1237	-0.0059	-0.0145	0.0516	-0.0221	0.1195	52.1131	18.3204	138.505
13	1.453	0.164	1.0916	2.912	0.36	0.8624	-0.0616	-0.1425	0.0582	0.0058	-0.0427	0.1538	-0.0256	-0.0852	0.1044	0.0999	0.0072	0.0152	0.1094	0.0119	0.1283	50.7157	10.3087	139.4958
14	3.6683	2.1375	-2.3388	3.4049	0.6399	4.6791	-0.1088	-0.062	0.0462	0.1474	-0.1644	0.0783	0.2417	-0.2772	0.2732	0.1028	-0.0309	0.0344	0.1185	0.0005	0.1045	50.3078	2.3075	141.9804
15	1.7696	-0.0593	2.4833	1.2216	-0.096	3.5178	0.0454	-0.0937	0.0324	-0.1112	-0.1206	0.1253	0.1272	-0.1813	0.0752	0.1171	-0.0703	0.0514	0.1283	-0.0191	0.149	49.7291	1.3366	134.7085
16	5.6993	-3.0456	2.2279	4.8229	-0.1903	1.1847	-0.059	0.2752	0.0771	0.0965	-0.0285	0.0583	-0.0197	0.1355	0.0876	0.0878	0.0027	-0.021	0.1294	-0.009	0.0982	51.2639	5.0439	128.0791
17	4.2504	-0.3844	2.2549	3.525	0.3556	1.4238	-0.0591	0.3152	0.0942	-0.367	-0.0732	0.2089	-0.1718	0.1259	0.1322	0.1458	-0.0242	-0.0186	0.1423	-0.007	0.0538	57.5165	10.5517	125.0867
18	2.2919	1.1137	1.1609	2.1795	-1.0528	3.1054	-0.0504	0.1163	0.0934	-0.0867	-0.0912	-0.0555	0.1405	0.149	0.1416	0.0987	-0.0233	0.0087	0.1154	0.0102	0.0873	61.372	10.794	130.7466
19	5.572	-1.8692	-3.4738	1.5562	-0.9319	6.9111	-0.08	-0.104	0.0813	0.0036	0.0824	-0.0546	0.137	-0.0145	-0.0024	0.1279	-0	-0.024	0.0991	-0.0029	0.0815	65.1444	9.5896	139.6006
20	0.4405	1.3198	-0.0722	4.1311	-0.5411	6.2799	0.0184	0.0817	-0.1003	0.273	0.2558	-0.3131	0.1503	0.311	-0.2742	0.2346	0.0647	-0.0804	0.0433	-0.0449	0.1103	65.3398	9.4619	148.7543
21	3.5539	6.0285	3.6485	10.4453	6.2831	3.7969	-0.5549	0.2154	0.1012	-0.5669	0.4085	0.3686	-0.3997	0.26	0.1465	0.677	0.065	0.2889	0.0639	0.0126	0.2857	76.9269	32.6143	134.8955
22	2.6828	-1.99	2.6941	5.1201	0.3384	4.2044	-0.2174	-0.0454	-0.3009	0.1047	0.3087	0.5186	-0.2763	0.1171	-0.0913	0.0411	0.0111	0.0334	0.0567	-0.0198	0.2069	71.0927	26.119	131.5384
23	2.1008	0.4477	0.609	0.2093	-0.9472	10.387	0.1008	0.2751	-0.0832	0.043	0.0692	-0.0024	-0.1263	-0.1314	-0.17	0.0491	-0.0144	-0.0192	0.0756	-0.0375	0.1934	68.4413	19.3766	125.9522
24	0.5273	-2.3459	0.2456	13.6998	1.9394	2.9683	-0.0613	-0.0356	-0.1417	0.1837	0.359	0.4136	-0.0734	0.1464	-0.2976	0.0641	0.0303	-0.0329	0.2272	-0.0683	0.1137	69.0674	20.2059	116.5004
25	12.4767	4.3338	-2.9713	2.7067	-2.6567	2.906	-0.094	0.5713	0.0215	0.2877	0.0622	-0.0097	-0.4247	0.0397	0.0319	0.1936	0.1	-0.0711	0.2348	-0.086	0.0416	75.0572	27.4281	116.996
26	6.1798	-0.54	2.7591	3.0204	-1.6722	3.0732	0.148	0.4244	-0.2521	0.0934	-0.2315	0.1563	-0.0796	0.1221	0.0834	0.0764	0.0174	-0.0164	0.1295	-0.0622	0.0791	79.2805	26.5235	123.936
27	2.617	-1.1284	-3.9128	0.7266	0.7619	9.4171	-0.0416	0.0843	-0.0493	0.1043	-0.0355	0.0205	-0.2514	-0.0962	0.0771	0.1029	-0.0131	-0.0222	0.0892	-0.0329	0.087	84.591	26.7487	130.2379
28	3.2516	-3.7148	0.392	6.7847	-0.5652	0.0641	-0.1258	0.0282	-0.0983	0.1758	0.1169	-0.1294	-0.0578	0.0195	0.009	0.1729	-0.049	-0.0333	0.1133	-0.0276	0.0665	89.2618	22.9732	135.8236
29	3.1031	0.8909	2.5132	2.3015	-0.2176	2.4711	0.0192	-0.02	0.0829	0.2084	-0.0344	0.2954	-0.1238	0.01	0.0152	0.0757	0.0149	0.0068	0.0895	-0.0637	0.2053	88.3007	15.2394	134.0123
30	5.2161	1.6052	-2.1755	0.6807	-0.1665	2.6106	0.1917	0.0513	-0.2408	0.041	-0.0181	-0.0432	-0.1695	0.1439	-0.1737	0.0158	-0.0032	-0.0146	0.0968	-0.163	0.3302	81.8109	8.7912	129.5639
31	3.1099	-2.2207	-1.3402	6.2227	-0.9486	1.3608	0.1391	0.384	-0.5292	-0.0579	-0.3978	0.3119	-0.0763	-0.1119	0.2587	0.032	0.0113	-0.0413	0.1123	-0.1251	0.1917	87.1063	5.0572	123.5403
32	1.0081	1.8518	-0.2523	8.748	0.603	0.3076	0.0095	0.1047	-0.053	-0.1725	-0.0213	-0.1103	-0.0278	-0.0137	0.0118	0.0601	0.0198	-0.0096	0.1429	-0.0484	0.0834	91.7509	12.8603	124.2799
33	5.2345	-1.2332	-0.2035	0.7807	0.3381	0.1854	0.1444	0.4217	-0.1216	-0.0426	-0.1749	0.0464	-0.0335	-0.0502	0.0305	0.1027	-0.0256	-0.0352	0.1606	-0.0284	0.0887	90.9051	21.4689	125.863
34	5.3295	-0.8671	2.6292	6.5088	-0.9584	4.8296	0.193	0.7995	0.4507	0.1153	-0.2925	-0.4326	-0.1401	0.2812	0.0995	0.0748	-0.0066	0.0284	0.1867	0.1017	0.0967	92.0673	29.3096	122.7916
35	4.822	0.9029	1.3964	4.4456	-0.4714	0.5316	0.3692	0.8215	0.3133	0.2791	-0.5433	-0.3659	0.0627	0.3443	0.1741	0.0953	0.084	-0.0312	0.3725	0.0579	0.0986	85.5225	25.3183	116.9391
36	2.4949	1.6146	-1.6103	8.9467	1.4552	1.8292	0.0679	-0.0165	-0.2712	-0.4699	-0.3125	0.0472	-0.208	-0.076	0.2446	0.0766	0.0274	-0.0362	0.1652	-0.0256	0.0439	85.4744	20.1674	113.2087
37	5.3453	1.3596	0.5589	0.9077	-1.1875	3.2051	-0.2056	0.2749	0.1425	-0.0173	0.163	0.0228	-0.1012	-0.1957	0.0427	0.0629	0.0494	-0.0581	0.1493	-0.0513	0.065	77.7068	17.8211	114.8026
38	0.3679	0.6012	-1.1416	6.9658	-3.553	4.031	0.012	0.0596	-0.1865	-0.2827	-0.2978	0.5763	0.0248	-0.0645	0.2859	0.0229	0.0363	-0.0792	0.1075	-0.1423	0.3191	77.8602	16.6668	121.7792
39	6.6782	-2.9514	-2.5087	4.1268	-0.5839	1.9585	0.0936	-0.1428	-0.52	0.351	-0.0517	0.5898	-0.2873	0.1185	-0.0419	0.1338	-0.021	0.0546	0.0716	-0.0466	0.1505	77.7131	18.576	131.2221
40	6.8658	2.2581	2.7695	1.0291	0.4989	2.262	0.0072	0.1748	-0.2934	0.1776	0.2119	-0.0804	-0.0907	-0.136	-0.2192	0.1876	0.0742	0.0146	0.1058	-0.0196	0.07	83.6289	17.6621	139.9058
41	3.8428	4.263	-1.6428	11.3838	-1.6611	0.7069	0.0451	0.5384	-0.0399	-0.2862	-0.0622	0.0002	-0.0313	-0.2414	0.0172	0.0535	0.0461	0.011	0.2459	0.004	0.0073	94.0227	20.6268	114.8233
42	5.9832	2.5699	0.299	2.0115	-2.7147	8.9223	0.0522	0.5949	-0.1865	-0.1597	0.1357	-0.0228	0.5912	0.3438	-0.1879	0.0833	0.0678	-0.0595	0.179	-0.1512	0.157	84.2331	6.9936	117.5276
43	4.3032	5.0115	0.3251	6.024	0.2095	0.1932	0.0053	-0.2286	0.2936	0.09	-0.172	0.2485	-0.0756	-0.0669	0.1667	0.0839	0.0275	0.0085	0.1328	-0.0072	0.2358	42.7231	6.5694	131.9292
44	5.8849	3.4348	0.4871	4.1402	2.1127	1.6104	0.175	0.3569	0.3742	-0.1174	-0.1395	0.1673	-0.1577	-0.2618	-0.0355	0.1442	0.0081	-0.0379	0.1174	0.0405	0.1225	55.1777	20.6174	129.8474

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	142 - 148
2	X-RAY DIFFRACTION	2	A	149 - 154
3	X-RAY DIFFRACTION	3	A	155 - 159
4	X-RAY DIFFRACTION	4	A	160 - 164
5	X-RAY DIFFRACTION	5	A	165 - 170
6	X-RAY DIFFRACTION	6	A	171 - 176
7	X-RAY DIFFRACTION	7	A	177 - 180
8	X-RAY DIFFRACTION	8	A	181 - 186
9	X-RAY DIFFRACTION	9	A	187 - 192
10	X-RAY DIFFRACTION	10	A	193 - 196
11	X-RAY DIFFRACTION	11	A	197 - 202
12	X-RAY DIFFRACTION	12	A	203 - 208
13	X-RAY DIFFRACTION	13	A	209 - 213
14	X-RAY DIFFRACTION	14	A	214 - 218
15	X-RAY DIFFRACTION	15	A	219 - 224
16	X-RAY DIFFRACTION	16	A	225 - 229
17	X-RAY DIFFRACTION	17	A	230 - 233
18	X-RAY DIFFRACTION	18	A	234 - 241
19	X-RAY DIFFRACTION	19	A	242 - 246
20	X-RAY DIFFRACTION	20	A	247 - 252
21	X-RAY DIFFRACTION	21	B	142 - 147
22	X-RAY DIFFRACTION	22	B	148 - 154
23	X-RAY DIFFRACTION	23	B	155 - 159
24	X-RAY DIFFRACTION	24	B	160 - 163
25	X-RAY DIFFRACTION	25	B	164 - 168
26	X-RAY DIFFRACTION	26	B	169 - 175
27	X-RAY DIFFRACTION	27	B	176 - 179
28	X-RAY DIFFRACTION	28	B	180 - 184
29	X-RAY DIFFRACTION	29	B	185 - 190
30	X-RAY DIFFRACTION	30	B	191 - 197
31	X-RAY DIFFRACTION	31	B	198 - 203
32	X-RAY DIFFRACTION	32	B	204 - 209
33	X-RAY DIFFRACTION	33	B	210 - 216
34	X-RAY DIFFRACTION	34	B	217 - 222
35	X-RAY DIFFRACTION	35	B	223 - 227
36	X-RAY DIFFRACTION	36	B	228 - 231
37	X-RAY DIFFRACTION	37	B	232 - 235
38	X-RAY DIFFRACTION	38	B	236 - 241
39	X-RAY DIFFRACTION	39	B	242 - 247
40	X-RAY DIFFRACTION	40	B	248 - 253
41	X-RAY DIFFRACTION	41	C	602 - 607
42	X-RAY DIFFRACTION	42	C	608 - 612
43	X-RAY DIFFRACTION	43	D	601 - 606
44	X-RAY DIFFRACTION	44	D	607 - 612

-
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