PDB-5o0o: Deglycosylated Nogo Receptor with native disulfide structure 5

ID or keywords:

Entry

Database: PDB / ID: 5o0o

Title

Deglycosylated Nogo Receptor with native disulfide structure 5

Components

Reticulon-4 receptor

Keywords

SIGNALING PROTEIN / nervous system / signaling / leucine-rich repeat domain / disulfide structure

Function / homology

Function and homology information

Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / regulation of postsynapse assembly / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / corpus callosum development ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Pronker, M.F. / Janssen, B.J.C.

Funding support

Netherlands, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction.
Authors: Pronker, M.F. / Tas, R.P. / Vlieg, H.C. / Janssen, B.J.C.

History

Deposition	May 16, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 15, 2017	Group: Database references / Structure summary / Category: audit_author / citation Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5o0o.cif.gz	1023.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5o0o.ent.gz	857 KB	Display	PDB format
PDBx/mmJSON format	5o0o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5o0o_validation.pdf.gz	550.7 KB	Display	wwPDB validaton report
Full document	5o0o_full_validation.pdf.gz	571.9 KB	Display
Data in XML	5o0o_validation.xml.gz	107.1 KB	Display
Data in CIF	5o0o_validation.cif.gz	151.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/5o0o ftp://data.pdbj.org/pub/pdb/validation_reports/o0/5o0o	HTTPS FTP

-
Related structure data

Related structure data	5o0kC 5o0lC 5o0mC 5o0nC 5o0pC 5o0qC 5o0rC 1oznS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ehq-2 4ihi-2 2ejl-2 2bjk-1 2bhp-1 4lem-d 1uzb-1 2ej6-2 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
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (5) #248 - Aug 2020 Phytosulfokine Receptor similarity (5) #68 - Aug 2005 Neurotrophins similarity (2) #105 - Sep 2008 Ribonuclease A similarity (2) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: Reticulon-4 receptor

B: Reticulon-4 receptor

C: Reticulon-4 receptor

D: Reticulon-4 receptor

E: Reticulon-4 receptor

F: Reticulon-4 receptor

G: Reticulon-4 receptor

H: Reticulon-4 receptor

hetero molecules

297 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	168.490, 168.490, 256.180
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein

Reticulon-4 receptor / Nogo receptor / NgR / Nogo-66 receptor / Nogo66 receptor-1 / NgR1

Mass: 36011.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Rtn4r, Ngr1, Nogor / Plasmid: pUPE107.03
Details (production host): secretion signal, C-terminal His6
Cell (production host): HEK293 / Cell line (production host): HEK293 GntI-/- / Organ (production host): KIDNEY / Production host:

Homo sapiens (human) / References: UniProt: Q99PI8

#2: Sugar

...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Chemical

...
ChemComp-CL / CHLORIDE ION

Mass: 35.453 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1765 / 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: 3.16 Å³/Da / Density % sol: 61.02 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 2.5 M sodium chloride, 100 mM Sodium Acetate/Acetic acid pH 4.5, 200 mM Lithium Sulfate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.2→70.39 Å / Num. obs: 185934 / % possible obs: 100 % / Redundancy: 8.5 % / CC_1/2: 0.998 / R_sym value: 0.131 / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 2.2 / CC_1/2: 0.667 / R_sym value: 0.956 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1OZN

1ozn

Resolution: 2.2→70.386 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.43

	R_factor	Num. reflection	% reflection
R_free	0.2073	9328	5.03 %
R_work	0.1667	-	-
obs	0.1687	185593	99.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→70.386 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19594	0	472	1765	21831

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	20612
X-RAY DIFFRACTION	f_angle_d	0.85	28057
X-RAY DIFFRACTION	f_dihedral_angle_d	13.174	7484
X-RAY DIFFRACTION	f_chiral_restr	0.031	3213
X-RAY DIFFRACTION	f_plane_restr	0.004	3667

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 (%)
2.2-2.225	0.2984	339	0.2463	5772	X-RAY DIFFRACTION	100
2.225-2.2512	0.303	305	0.2378	5819	X-RAY DIFFRACTION	100
2.2512-2.2786	0.2896	305	0.2387	5797	X-RAY DIFFRACTION	100
2.2786-2.3075	0.2722	299	0.2158	5834	X-RAY DIFFRACTION	100
2.3075-2.3379	0.2598	291	0.213	5832	X-RAY DIFFRACTION	100
2.3379-2.3699	0.2871	320	0.2181	5771	X-RAY DIFFRACTION	100
2.3699-2.4037	0.2775	336	0.2143	5802	X-RAY DIFFRACTION	100
2.4037-2.4396	0.275	336	0.2113	5788	X-RAY DIFFRACTION	100
2.4396-2.4777	0.2592	291	0.2087	5870	X-RAY DIFFRACTION	100
2.4777-2.5184	0.2221	283	0.1955	5852	X-RAY DIFFRACTION	100
2.5184-2.5618	0.2137	308	0.1879	5831	X-RAY DIFFRACTION	100
2.5618-2.6084	0.2285	307	0.1875	5809	X-RAY DIFFRACTION	100
2.6084-2.6586	0.2476	286	0.1852	5861	X-RAY DIFFRACTION	100
2.6586-2.7128	0.2288	313	0.1806	5884	X-RAY DIFFRACTION	100
2.7128-2.7718	0.2364	318	0.1794	5809	X-RAY DIFFRACTION	100
2.7718-2.8363	0.2176	305	0.1781	5858	X-RAY DIFFRACTION	100
2.8363-2.9072	0.2501	302	0.1862	5855	X-RAY DIFFRACTION	100
2.9072-2.9858	0.252	349	0.197	5826	X-RAY DIFFRACTION	100
2.9858-3.0737	0.2268	322	0.1891	5849	X-RAY DIFFRACTION	100
3.0737-3.1729	0.2427	293	0.185	5890	X-RAY DIFFRACTION	100
3.1729-3.2863	0.1894	277	0.1765	5911	X-RAY DIFFRACTION	100
3.2863-3.4179	0.2243	304	0.1681	5895	X-RAY DIFFRACTION	100
3.4179-3.5734	0.1997	314	0.154	5892	X-RAY DIFFRACTION	100
3.5734-3.7618	0.1833	278	0.1361	5948	X-RAY DIFFRACTION	100
3.7618-3.9975	0.1586	321	0.1279	5924	X-RAY DIFFRACTION	100
3.9975-4.3061	0.1656	315	0.125	5931	X-RAY DIFFRACTION	100
4.3061-4.7393	0.1568	321	0.1226	5961	X-RAY DIFFRACTION	100
4.7393-5.4249	0.1574	326	0.1282	6003	X-RAY DIFFRACTION	100
5.4249-6.8339	0.1837	327	0.1523	6051	X-RAY DIFFRACTION	100
6.8339-70.422	0.1715	337	0.1706	6140	X-RAY DIFFRACTION	97

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	9.6461	6.5336	-4.4432	4.5478	-3.7794	6.9066	0.141	-0.1295	0.4905	-0.1305	0.1189	1.5815	0.0014	-1.2115	-0.0996	0.3076	-0.053	-0.0104	0.4949	0.004	0.7292	-3.085	104.3394	138.1165
2	3.1484	-0.0498	0.1363	1.3856	-0.658	3.1681	0.1208	-0.1733	-0.129	0.139	-0.0841	0.2649	0.1649	-0.2455	-0.0366	0.2581	-0.0751	0.0018	0.2243	-0.0012	0.4607	11.4167	97.0473	138.0371
3	3.8499	0.195	2.0155	3.6754	-0.7687	3.6593	0.054	-0.0367	-0.166	0.0428	0.1189	0.3433	0.1819	-0.0053	-0.1619	0.2	-0.0088	0.0341	0.1867	-0.0139	0.3022	30.5673	101.2972	144.2015
4	4.9154	-0.7092	2.6355	3.4288	-0.9982	3.0944	-0.0476	-0.0988	-0.0312	0.0614	0.0632	0.0602	0.0632	0.0702	-0.0165	0.1982	0.0108	0.0539	0.204	0.0054	0.1448	42.9451	108.8032	156.4355
5	3.4121	-5.4456	-1.2424	9.5347	0.8785	7.1989	-0.3633	-0.8177	-0.5964	1.019	0.3001	0.3675	0.3252	0.5521	0.1116	0.3548	0.0367	0.0411	0.5505	0.0598	0.3092	52.6754	102.8134	168.884
6	7.6213	-3.7974	-1.8694	3.3975	-0.9738	2.8915	-0.3078	-0.7191	0.0159	0.2423	0.3176	-0.4224	0.1188	0.2284	-0.0389	0.3604	0.0442	-0	0.4208	0.0579	0.3025	63.2065	95.4121	158.2671
7	3.4257	0.1168	-0.1202	1.6352	0.3579	3.428	0.0548	-0.186	0.0222	0.0721	-0.0683	-0.3948	-0.1617	0.3092	0.0091	0.2377	-0.0577	-0.0163	0.2071	0.0226	0.3913	75.8787	156.7966	138.5353
8	3.1415	0.6946	-1.8594	0.877	-0.691	2.135	-0.0694	-0.0509	0.2101	0.0886	0.0431	-0.0285	-0.1131	-0.1223	0.0253	0.2504	0.0451	-0.0364	0.197	-0.0535	0.2703	47.1003	149.5223	151.5024
9	9.2756	-6.5974	3.4698	2.0007	-4.7472	2.2802	-0.1351	-0.9509	0.1816	0.338	0.4417	0.6428	-0.2917	0.0955	-0.2747	0.4824	0.2191	0.0031	0.5292	-0.2051	0.293	26.4901	152.963	163.6932
10	3.4921	0.6071	0.4746	2.6006	-1.1279	4.3531	0.0399	0.4768	0.1598	-0.0885	0.0814	0.4279	-0.1908	-0.6544	-0.1463	0.2697	0.147	-0.1087	0.4371	-0.0469	0.4421	3.7215	156.2734	114.3616
11	2.4877	-0.4603	-1.3778	0.5709	0.4524	1.63	-0.0491	0.0594	0.2354	-0.0591	0.0307	-0.015	-0.1914	-0.0447	0.0143	0.2781	0.0379	-0.1209	0.2316	0.0121	0.3373	25.8587	154.3241	111.6995
12	6.1301	1.2131	-2.7522	2.7617	-0.3497	3.1422	-0.0681	0.1863	0.184	-0.1	-0.0161	-0.0796	-0.0294	0.1078	0.0696	0.2197	0.0147	-0.0787	0.2429	0.0379	0.2623	44.2199	145.2372	97.7642
13	6.9004	2.6201	-1.0014	2.4423	-1.6091	8.1398	-0.2397	1.1818	0.336	-0.5723	0.3561	-0.1059	-0.582	0.2857	-0.0733	0.3981	-0.0692	-0.0025	0.6041	0.1277	0.328	53.7898	149.075	85.4102
14	3.906	3.6216	-3.4027	3.3558	-3.1323	3.058	0.2107	0.7933	0.6965	-0.0883	-0.1071	-0.9907	-0.475	0.7742	-0.04	0.4895	-0.0739	-0.0207	0.68	0.1792	0.7213	64.4819	158.9426	95.8682
15	8.1654	-0.2533	3.19	3.0328	-1.2828	6.1287	0.1931	-0.4522	-0.6161	0.2328	0.2038	0.4486	0.5909	-0.2172	-0.3655	0.3725	0.0747	0.0531	0.2137	0.0395	0.2169	71.9537	81.9304	147.0383
16	0.9603	-0.2047	0.4384	2.8075	0.1231	2.757	-0.0768	-0.1306	0.0124	0.1268	0.0424	-0.0367	0.1359	0.1113	0.0262	0.1841	0.0573	0.0267	0.2234	-0.0009	0.1842	73.5453	95.672	142.5139
17	3.3479	-0.3551	0.656	4.9405	1.37	3.437	-0.0264	0.0567	0.1758	-0.0706	0.0279	-0.1449	-0.13	0.1283	-0.0034	0.1574	0.0296	0.0356	0.2035	0.0158	0.2031	69.2954	113.7157	146.0308
18	6.5325	1.4888	1.0079	7.1035	-0.7477	6.0128	-0.0356	0.0456	0.5495	-0.2406	0.0089	-0.1089	-0.2102	0.1897	0.0395	0.1797	0.0694	0.0454	0.1101	-0.0508	0.2173	64.0138	123.6121	150.2848
19	2.6997	1.0537	0.7798	6.599	2.328	2.2047	-0.119	-0.4619	0.4755	0.5163	-0.0672	-0.0158	-0.1169	-0.1016	0.1673	0.289	0.0352	-0.0245	0.2725	-0.0872	0.2726	60.9354	131.3042	161.0031
20	4.4951	3.8348	-0.2971	7.1278	-0.9923	2.2369	0.0885	-0.5259	0.8783	0.6426	-0.3072	-0.8323	-0.5334	1.2097	0.235	0.4803	-0.07	-0.1558	0.6296	-0.0165	0.8021	75.078	145.4685	156.6449
21	6.783	6.7765	-6.3841	6.7778	-6.3909	6.0404	0.0749	-0.0686	1.4846	-0.0802	0.3437	0.8442	-0.6763	-0.3584	-0.3478	0.5118	0.0323	-0.0367	0.3927	0.0182	0.6163	68.1137	175.0563	109.1441
22	0.5947	0.4462	0.1128	3.746	-0.1313	3.2193	-0.0938	0.2232	0.0231	-0.1001	0.0405	-0.1241	-0.1696	0.0023	0.051	0.2118	-0.037	0.0028	0.2749	0.0145	0.3878	74.6405	160.5477	112.3112
23	2.3252	0.5927	-0.2616	3.8141	1.3687	3.9484	0.072	-0.0595	0.0782	0.0999	0.0406	-0.2545	0.0852	0.201	-0.091	0.1659	-0.0091	-0.0145	0.2418	0.0124	0.3325	69.9622	140.5318	109.5194
24	5.1923	-1.5143	-1.4857	9.0102	0.8133	7.5103	0.1073	-0.3113	-0.1726	0.324	-0.1309	-0.281	0.2797	0.4279	0.0303	0.1304	-0.0477	-0.0569	0.2091	0.0156	0.209	65.3084	129.6254	104.1174
25	4.5615	-2.3365	1.0407	9.7578	-5.9472	3.7184	-0.1873	-0.1029	0.152	-0.1839	0.1311	0.1264	0.2381	-0.1339	0.0136	0.2678	-0.033	-0.0408	0.2417	-0.0663	0.2598	57.3401	129.7303	102.2135
26	7.4707	-2.8638	-0.8097	4.4844	0.3201	4.5651	0.0433	0.5283	-0.3972	-0.3161	-0.2185	0.1145	-0.0939	0.1148	0.1774	0.2371	-0.0238	0.0142	0.2826	-0.0443	0.2428	63.1302	122.3423	93.5321
27	8.7257	-4.2671	-2.9273	7.2983	1.4497	7.7637	-0.0312	0.74	-0.2275	-0.6383	-0.4097	-0.5754	0.4242	0.7407	0.3879	0.4298	-0.0105	0.141	0.4998	-0.0222	0.3236	69.1793	114.6312	88.3107
28	4.2773	-5.3664	-1.5879	8.8815	-0.8682	5.9181	-0.6504	-0.2334	-1.1529	-0.5172	0.3687	0.2379	0.5621	1.1264	0.3062	0.3645	0.0557	0.1679	0.58	0.0848	0.5368	76.0009	107.027	102.7181
29	3.369	0.3782	0.3051	4.2937	1.3871	2.2541	0.0493	0.1589	-0.0248	-0.1878	-0.0048	-0.4279	0.0615	0.3386	-0.0506	0.1896	0.0836	0.0145	0.2407	0.0259	0.1848	83.1053	97.9365	117.2215
30	2.4209	-0.1414	1.5095	0.3661	-0.2293	1.5365	0.0319	0.0478	-0.0662	-0.0278	0.01	0.0717	0.0734	0.0052	-0.0363	0.2029	0.0386	0.042	0.1902	-0.0043	0.1941	61.0081	99.5363	113.4353
31	5.6125	0.8765	2.1401	3.6933	0.7137	3.5399	-0.0997	0.1786	-0.0409	-0.1198	0.0088	0.3215	0.0018	-0.1487	0.0835	0.1809	0.0316	0.0096	0.2347	-0.0104	0.1873	43.2863	107.8385	98.4092
32	6.5099	0.0531	0.3713	8.9696	-0.3986	9.2286	-0.1207	1.0102	-1.0063	-0.6955	-0.191	0.5294	0.4671	-0.7406	0.2572	0.3288	0.009	-0.0758	0.6243	-0.1538	0.3447	33.9488	103.1685	85.1946
33	5.3991	5.2961	3.5098	9.1982	1.0919	3.8382	0.0846	1.2161	-0.9659	-0.1576	-0.2416	0.7136	1.1329	-0.0139	0.0373	0.5469	-0.0175	0.0788	0.5568	-0.222	0.6985	23.4422	93.7402	96.7416
34	1.9824	0.7269	0.4629	3.2569	0.5659	3.1701	0.0189	0.2011	-0.2934	-0.1314	0.0956	-0.1152	0.4265	0.0182	-0.1055	0.2761	-0.0444	-0.0518	0.2344	-0.0276	0.4484	12.9056	91.3842	111.7184
35	2.119	0.5586	-0.465	3.2074	-1.7114	3.0653	-0.0045	0.0635	-0.0127	0.0536	0.0544	0.3208	-0.1069	-0.1593	-0.0217	0.1769	0.0026	-0.0315	0.2615	-0.0545	0.3845	18.1258	115.2513	107.547
36	3.9484	-1.3595	0.2785	7.4228	-2.3725	1.6639	-0.0126	0.3012	0.2226	-0.4087	-0.1107	0.2751	-0.0055	0.0259	0.1125	0.2275	0.0086	-0.0774	0.2939	-0.0302	0.2438	25.1531	130.0656	93.1086
37	2.5054	0.3892	-1.9421	0.195	-0.1627	1.7628	-0.2498	0.282	0.7057	-0.4833	0.1103	0.3389	-0.5949	-0.9192	-0.0483	0.4769	0.0738	-0.1708	0.5964	-0.0181	0.6764	11.6306	145.458	97.2623
38	5.9472	-5.8937	-5.8212	6.0133	5.724	5.7124	0.2656	-0.1039	1.7588	0.0808	0.1786	-0.5638	-1.1808	-0.0085	-0.3948	0.804	0.1236	-0.1327	0.4507	-0.0768	0.6107	17.8303	175.3951	143.7693
39	0.8382	-0.2113	0.3231	2.8316	-0.2104	1.8712	-0.1615	-0.2546	0.127	0.1182	-0.009	0.2557	-0.3578	-0.2891	0.1496	0.2999	0.139	-0.0775	0.344	-0.1031	0.3699	11.1493	160.6797	140.776
40	5.9873	0.7033	-5.3315	4.8313	0.128	7.9587	-0.0845	0.5518	-0.4356	-0.1524	-0.1031	0.5649	0.2019	-0.7289	0.1907	0.2247	0.0786	-0.0924	0.3103	-0.0393	0.3408	11.9488	145.9619	140.3709
41	5.4781	1.3689	-0.4745	5.2993	-2.3391	4.1218	0.0381	-0.0871	-0.0066	-0.0728	-0.0211	0.19	0.0836	-0.2046	-0.0127	0.1914	0.0652	-0.013	0.2331	-0.0736	0.2922	17.5381	139.2688	145.2306
42	2.3469	1.7095	-2.5385	4.0076	-0.9086	9.0589	-0.0737	0.2678	-0.3173	-0.0452	0.0263	0.2518	0.5132	-0.5188	0.0651	0.1709	0.0504	-0.0007	0.2397	-0.0307	0.3311	20.965	130.1377	149.9066
43	5.2909	4.9354	4.0564	8.8548	5.3462	3.8688	-0.0281	0.0539	-0.1451	0.2384	0.0617	-0.4421	0.63	0.0677	-0.0334	0.3019	0.0452	0.0434	0.2467	0.0649	0.2727	28.9169	130.1583	151.8681
44	6.7353	1.7138	-0.9027	4.601	-1.8299	2.9919	-0.2205	-0.3964	-0.9131	0.1224	-0.1228	0.1793	0.1898	-0.1501	0.3297	0.3393	0.0181	0.115	0.332	-0.0046	0.3871	22.6538	121.6185	159.5975
45	1.9102	2.7361	0.5617	7.8824	-2.0806	2.2859	-0.057	-0.7501	-0.2214	0.7164	0.0713	0.6806	0.094	-0.1877	-0.0087	0.4273	0.0747	0.1967	0.4557	0.069	0.398	22.8188	122.4797	166.1807
46	5.9215	4.3183	0.817	5.9654	0.6701	5.737	0.17	0.0658	-0.8461	0.3379	0.2003	1.0066	1.384	-1.2629	-0.3501	0.5532	-0.1841	0.1607	0.6415	-0.0424	0.836	11.1273	108.9175	154.4
47	1.8933	-1.7581	1.9018	3.8387	-5.6837	9.1245	-0.2913	-1.204	2.2096	1.3874	0.4703	-1.0921	-1.8233	1.0036	0.1506	0.8759	0.0948	0.1572	1.1138	0.022	0.7973	30.4469	167.4151	162.0214
48	2.7897	-4.5868	1.1923	8.4885	-4.6973	9.3653	-0.0082	-0.4402	-0.1885	0.2891	0.2414	0.9109	-0.2912	-0.2034	-0.4489	0.3918	0.0223	0.0217	0.4081	-0.0954	0.3969	21.5058	159.8974	156.9315

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 136 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 137 through 213 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 214 through 290 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 291 through 320 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 321 through 342 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 26 through 136 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 137 through 305 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 306 through 311)
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 26 through 83 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 84 through 213 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 214 through 290 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 291 through 318 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 319 through 342 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 25 through 57 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 58 through 136 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 137 through 213 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 214 through 237 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 238 through 305 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 306 through 341 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 24 through 39 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 40 through 136 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 137 through 213 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 214 through 242 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 243 through 256 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 257 through 290 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 291 through 320 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 321 through 341 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 26 through 83 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 84 through 213 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 214 through 290 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 291 through 319 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 320 through 341 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 26 through 136 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 137 through 237 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 238 through 305 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 306 through 342 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 25 through 39 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 40 through 136 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 137 through 156 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 157 through 213 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 214 through 242 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 243 through 256 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 257 through 277 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 278 through 305 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 306 through 341 )
47	X-RAY DIFFRACTION	47	chain 'B' and (resid 312 through 318)
48	X-RAY DIFFRACTION	48	chain 'B' and (resid 319 through 342)

-
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