PDB-8w4e: Crystal structure of the sigma-1 receptor from Xenopus laevis in ...

ID or keywords:

Entry

Database: PDB / ID: 8w4e

Title

Crystal structure of the sigma-1 receptor from Xenopus laevis in the absence of known ligands (C2 form)

Components

Sigma non-opioid intracellular receptor 1

Keywords

MEMBRANE PROTEIN / sigma receptor / S1R / endogenous ligand / neurosteroid / P4

Function / homology

Function and homology information

nuclear outer membrane / nuclear inner membrane / lipid transport / cytoplasmic vesicle / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function

Biological species

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.805 Å

Authors

Xiao, Y. / Fu, C. / Sun, Z. / Zhou, X.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Insight into binding of endogenous neurosteroid ligands to the sigma-1 receptor.
Authors: Fu, C. / Xiao, Y. / Zhou, X. / Sun, Z.

History

Deposition	Aug 23, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8w4e.cif.gz	536.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8w4e.ent.gz	451.2 KB	Display	PDB format
PDBx/mmJSON format	8w4e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w4/8w4e ftp://data.pdbj.org/pub/pdb/validation_reports/w4/8w4e	HTTPS FTP

-
Related structure data

Related structure data	8w4bC 8w4cC 8w4dC 8wueC 8wwbC 8ybbC C: citing same article (ref.)
Similar structure data	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: Sigma non-opioid intracellular receptor 1

B: Sigma non-opioid intracellular receptor 1

C: Sigma non-opioid intracellular receptor 1

D: Sigma non-opioid intracellular receptor 1

E: Sigma non-opioid intracellular receptor 1

F: Sigma non-opioid intracellular receptor 1

154 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sigma non-opioid intracellular receptor 1

B: Sigma non-opioid intracellular receptor 1

C: Sigma non-opioid intracellular receptor 1

defined by author&software
77.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Sigma non-opioid intracellular receptor 1

E: Sigma non-opioid intracellular receptor 1

F: Sigma non-opioid intracellular receptor 1

defined by author&software
77.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.697, 145.688, 145.886
Angle α, β, γ (deg.)	90.00, 107.43, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Sigma non-opioid intracellular receptor 1 Mass: 25720.322 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: sigmar1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q6DCU6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.95 Å³/Da / Density % sol: 58.26 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.32M LiCl, 0.1M Na+-citrate pH 5.5, 12% PEG 4000, 10% glycerol, 15mM Na+-cholate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.5→45.141 Å / Num. obs: 44588 / % possible obs: 72.2 % / Redundancy: 6.7 % / R_merge(I) obs: 0.074 / R_pim(I) all: 0.031 / R_rim(I) all: 0.081 / Net I/σ(I): 13.5 / Num. measured all: 297941
Reflection shell	Resolution: 2.5→2.678 Å / % possible obs: 19.4 % / Redundancy: 6.8 % / R_merge(I) obs: 1.124 / Num. measured all: 15150 / Num. unique obs: 2230 / R_pim(I) all: 0.462 / R_rim(I) all: 1.217 / Net I/σ(I) obs: 1.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
Aimless	0.7.4	data scaling
XDS	BUILT 20220820	data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.805→45.141 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2681	2226	5.1 %
R_work	0.243	-	-
obs	0.2443	43683	99.82 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.805→45.141 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10535	0	0	3	10538

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	10799
X-RAY DIFFRACTION	f_angle_d	0.428	14672
X-RAY DIFFRACTION	f_dihedral_angle_d	11.698	6140
X-RAY DIFFRACTION	f_chiral_restr	0.036	1669
X-RAY DIFFRACTION	f_plane_restr	0.003	1796

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 (%)
2.8054-2.8664	0.4603	148	0.3832	2575	X-RAY DIFFRACTION	100
2.8664-2.9331	0.381	147	0.3646	2557	X-RAY DIFFRACTION	100
2.9331-3.0064	0.3746	147	0.3658	2595	X-RAY DIFFRACTION	100
3.0064-3.0877	0.3461	133	0.3523	2575	X-RAY DIFFRACTION	100
3.0877-3.1785	0.3286	109	0.3016	2628	X-RAY DIFFRACTION	100
3.1785-3.2811	0.3067	154	0.3026	2564	X-RAY DIFFRACTION	100
3.2811-3.3983	0.3278	126	0.2901	2600	X-RAY DIFFRACTION	100
3.3983-3.5343	0.3238	122	0.2801	2575	X-RAY DIFFRACTION	100
3.5343-3.6951	0.2687	141	0.2648	2586	X-RAY DIFFRACTION	100
3.6951-3.8898	0.2608	139	0.258	2610	X-RAY DIFFRACTION	100
3.8898-4.1334	0.2595	129	0.2382	2592	X-RAY DIFFRACTION	100
4.1334-4.4523	0.2748	151	0.2261	2579	X-RAY DIFFRACTION	100
4.4523-4.8998	0.2428	150	0.2007	2580	X-RAY DIFFRACTION	100
4.8998-5.6077	0.2738	134	0.2286	2623	X-RAY DIFFRACTION	100
5.6077-7.0607	0.2547	143	0.2551	2591	X-RAY DIFFRACTION	100
7.0607-45.141	0.2154	153	0.1871	2627	X-RAY DIFFRACTION	99

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	5.1287	-1.7614	1.8718	5.0184	0.9064	7.6235	-0.3932	-0.0292	-0.0038	0.2274	-0.4033	0.9936	-0.0661	-0.1789	0.8956	0.6231	0.0551	0.1381	0.8481	0.0011	0.9742	1.4224	-27.673	42.216
2	1.7485	0.5688	-1.2653	0.5133	-0.35	2.5921	0.4325	0.7011	-0.1208	-0.6302	-0.1942	0.0051	0.4235	-0.4737	-0.2341	1.2717	0.5275	-0.1722	1.3192	-0.0797	0.6402	18.9817	-40.1183	12.0272
3	0.1935	0.8212	-0.4605	5.059	0.3863	3.9566	0.8613	3.0709	-0.5466	-0.1001	-1.1104	1.0476	0.1958	-0.6123	0.274	0.8209	0.3079	-0.0625	1.2714	-0.0447	0.6984	18.0921	-38.0795	29.1782
4	0.2661	0.7442	-0.2087	2.2688	-0.2247	3.208	0.3536	0.2939	-0.5257	-0.9614	-0.1283	0.4921	1.143	0.4474	-0.2004	0.8186	0.3114	-0.1147	0.9793	-0.178	0.8003	18.7947	-48.7776	28.4518
5	0.3972	0.3246	-0.156	3.0963	0.1651	2.7642	0.4487	0.0159	-0.6897	-0.3472	-0.6159	0.634	1.5771	0.6235	0.0688	1.1242	0.2125	0.008	0.8248	-0.1421	0.581	17.5557	-44.1119	27.9616
6	0.8407	0.1562	-1.2048	3.9533	-0.0573	1.819	0.4315	1.0798	0.1882	-1.1588	-0.6059	0.3723	0.3532	-0.2386	0.4283	1.2255	0.529	-0.197	1.3171	0.0677	0.8387	16.7138	-29.422	16.4293
7	3.0764	0.3832	-2.7828	5.6872	-1.6495	5.9363	-0.0512	0.359	0.1528	0.2251	0.0436	-0.7652	-1.3713	-0.3507	0.144	0.9569	-0.0794	-0.2327	0.8285	0.1252	0.9732	29.5516	-8.7534	47.7931
8	1.425	1.3459	-0.1361	2.7924	-0.9519	1.3261	-0.304	-0.7144	0.0339	-0.0006	0.0392	0.3879	-0.0234	0.3462	0.1359	0.9183	0.0441	0.0166	1.0536	0.0006	0.8453	16.1019	-28.9747	66.7901
9	3.6968	0.9056	-0.4695	2.9202	-1.1305	3.712	0.0766	-0.1676	-0.4716	-0.04	-0.1103	0.3702	0.7379	-0.1905	0.0759	0.862	0.104	0.1427	0.6868	-0.0034	0.7707	14.0998	-45.5533	55.225
10	2.8572	-0.7254	-0.8621	3.0952	-1.3039	1.0632	-0.2209	-0.0458	0.1674	0.66	0.1041	-0.4441	0.0073	-0.022	0.1138	0.8402	0.1263	-0.0867	0.8425	-0.0032	0.6807	26.0918	-36.527	51.6638
11	0.0322	0.1481	-0.1849	2.1891	-0.204	0.3341	-0.0173	-0.0115	0.2681	0.7898	-0.0797	-1.43	0.2229	0.803	0.0375	0.9629	0.1258	-0.1185	0.9346	0.1165	0.8414	30.9433	-38.5648	55.3686
12	1.5921	0.2886	0.3999	3.2776	-1.0206	1.2798	0.1043	0.4701	-0.2187	0.2284	-0.2953	-0.3215	-0.1179	-0.2097	0.1587	0.6832	0.1891	-0.0029	0.8421	0.0335	0.7685	19.5346	-34.0718	47.3257
13	4.4012	-1.6728	-2.1749	5.153	-1.4652	5.5115	-0.4505	-0.3014	-1.2734	1.1247	-0.1137	0.2261	-0.2287	-0.5892	0.5708	0.8228	0.1547	0.0147	0.9204	0.0809	0.9572	3.166	-33.9711	54.0527
14	4.8675	2.3627	0.4805	3.1526	0.2426	2.612	-0.2192	0.5882	0.5357	-1.1831	-0.0174	-0.0995	-0.5954	-0.2447	0.2586	1.3936	0.419	0.2108	1.1155	0.0402	0.9049	19.5353	-16.1295	16.3015
15	1.4209	-2.1368	0.2171	3.2618	0.2065	2.2744	-0.218	0.5894	0.5788	-0.1827	-0.0076	-1.053	-0.4529	0.7102	0.1306	0.7901	-0.1531	0.261	1.1891	0.0669	1.5716	53.185	-19.9352	31.7052
16	3.7213	1.4136	-1.4918	2.6399	0.8933	2.2493	0.6312	-0.0414	0.4494	-0.1588	-0.1443	-0.3619	-0.3382	-0.0776	-0.4122	0.8068	0.1593	0.0029	0.7214	0.1031	1.2153	44.7974	-21.618	39.7461
17	2.476	0.8576	0.381	1.7622	0.8449	2.2729	0.4786	0.7918	-0.2156	-0.6802	-0.1689	-0.8765	-0.5213	0.582	-0.3716	0.943	0.3475	0.1527	1.0521	0.2531	1.1614	42.3352	-34.4973	26.4975
18	0.5703	0.551	0.3524	0.9001	-0.6062	2.1189	-0.2015	1.3461	0.0916	-0.4891	-0.4118	-0.5335	-0.1807	0.9841	0.7449	1.0053	0.4287	0.1066	1.3096	0.1317	1.2026	43.8054	-26.8618	25.116
19	0.8916	-0.6219	1.2659	1.542	0.2637	0.8593	0.1888	0.1886	0.4052	-0.0988	-0.251	-0.6364	-0.0839	0.2913	0.1205	0.8568	0.1323	0.1497	0.8725	0.1109	1.1901	38.5014	-17.105	39.5446
20	2.7036	-1.4958	0.7961	6.5936	1.0837	6.1553	-0.3649	-0.25	0.0519	0.3372	0.0414	1.454	0.428	-0.2583	0.4202	0.6595	0.0108	-0.0269	0.7325	0.0293	0.9835	-3.337	-17.9285	41.3598
21	1.7931	-0.8252	1.1395	3.3762	-0.2049	5.8819	-0.2422	-0.4662	0.1321	0.6506	-0.0602	-0.4491	-0.5657	-0.39	0.2622	1.1077	0.266	-0.1698	0.8858	-0.0539	0.7468	5.6226	11.5576	62.0179
22	2.2733	-0.0268	1.8907	2.6512	1.4846	2.8848	0.1064	-0.0082	-0.6301	-0.0559	-0.7229	1.1997	0.4641	-0.5287	0.6127	1.0228	0.2401	0.1064	0.7559	-0.0614	0.9033	-6.0017	7.562	48.9665
23	0.2987	0.8803	0.1022	2.6287	0.9836	1.3382	0.5518	0.4304	0.233	0.0041	-0.7012	0.9763	-0.0872	-0.1323	0.2681	0.9363	0.2499	0.0893	0.9877	-0.0731	0.8752	-9.2131	8.5433	53.661
24	2.4426	0.3445	-0.3004	1.7713	0.9624	1.091	-0.5387	-0.0883	0.0732	0.6075	-0.2112	0.536	-0.4492	-0.283	0.6445	0.9251	0.305	0.0335	0.7909	0.0101	0.7519	4.8113	5.7845	49.6681
25	2.0043	-1.6794	-1.1604	4.2651	-1.0659	3.0222	-0.9972	0.0502	-0.3293	1.1661	-0.8407	-0.6706	-1.5202	-0.5602	1.6942	1.0029	0.2489	-0.1025	0.7878	0.0019	0.8468	17.4652	3.2776	61.8382
26	4.8959	1.3319	0.7079	4.584	-0.0065	1.7161	0.3125	0.2432	-0.2546	-1.009	-0.2526	-0.2178	0.2132	0.3949	-0.0128	1.3046	0.4599	0.2571	1.1642	0.1159	0.803	17.5605	-4.1661	17.4117
27	2.8616	-0.0558	1.6005	5.3274	-0.959	3.6516	-0.5323	0.7351	-0.3901	-1.5281	0.8053	2.0145	-0.0415	-0.0595	-0.4061	1.1185	0.091	-0.306	0.9127	-0.0437	1.8009	-19.3801	-2.7141	18.9573
28	3.0132	0.6063	-0.0144	3.0058	-0.02	3.2643	0.35	0.365	-0.26	-0.4603	-0.2114	1.0701	0.3842	-0.4502	-0.1391	0.9082	0.2075	-0.2806	0.9243	-0.1434	1.3984	-14.9732	-3.2835	30.2549
29	2.433	1.2171	-0.1265	1.9403	-0.6081	1.221	0.2142	0.3983	0.2081	-1.3202	-0.0446	1.2278	0.6401	0.294	-0.1245	0.9773	0.3215	-0.2814	1.0411	-0.0494	1.0318	-9.2207	10.3697	21.4273
30	3.4063	1.5706	2.356	1.9569	-0.7978	4.6971	-0.3346	0.752	0.476	0.414	-0.1794	1.9285	-0.7962	0.8786	0.2867	0.6642	0.3256	-0.0422	0.934	0.1476	1.0905	-5.1847	7.4027	24.3325
31	0.8746	0.5104	-1.3562	1.5954	0.1555	1.7269	-0.0067	0.5188	-0.4832	-0.1152	-0.1651	0.7637	0.3151	-0.385	0.0423	1.034	0.1412	-0.2034	0.9804	-0.1726	1.2902	-8.7813	-10.1397	31.2414
32	5.9331	0.2886	-1.3974	6.5647	-2.1114	7.2053	-0.0012	-0.1075	0.2353	0.9245	-0.0821	-0.7752	-1.1746	-0.1835	-0.0272	0.7757	0.0889	-0.1651	0.6791	-0.0586	0.6893	23.2881	-0.3684	51.0823
33	2.8747	0.5388	-0.2658	4.6009	0.2362	2.3234	0.3839	0.6812	0.4478	-0.4476	-0.0838	-0.5572	-0.4757	0.2202	-0.2427	1.1286	0.3901	0.3174	1.0892	0.2681	1.012	18.7168	20.288	19.9202
34	2.9667	0.5609	-0.2134	2.1164	-0.1161	2.1576	-0.1103	0.7518	-0.3829	0.5359	-0.2449	-0.7662	-0.6793	0.4876	0.322	0.8883	0.255	0.0816	0.9758	0.2636	0.9191	14.4563	14.8806	34.9966
35	1.4039	0.6035	-1.1601	1.9204	-0.7289	3.8234	0.184	-0.0152	0.3419	0.5387	-0.2018	-0.4275	-0.9094	-0.0342	0.0827	0.7862	0.1745	0.0155	0.8363	0.1406	0.8914	10.9098	24.1501	38.0753
36	0.2742	-0.1288	0.3003	0.2384	-0.0112	0.6435	-0.2994	0.1112	0.0326	1.2009	0.6474	0.1733	-0.7495	0.0524	-0.4569	1.2088	0.2126	-0.0291	0.8666	0.2195	1.1435	17.2329	24.3479	35.2257
37	2.2057	0.536	-0.3775	3.8858	-0.5887	1.8798	0.6461	0.373	-0.1038	-0.0786	-0.6295	-0.4434	-0.663	-0.2987	0.0272	0.9488	0.2151	0.0433	0.9003	0.0445	0.8931	13.7702	11.8402	29.6465
38	3.5802	0.6896	-0.6376	1.1196	-1.0459	3.0932	0.0762	0.7323	-0.414	-1.1603	-0.6702	-1.1955	-0.3877	-0.0354	0.5403	1.3777	0.4113	0.4527	1.0561	0.2477	1.2143	23.8166	7.5438	15.1867

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 106 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 118 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 119 through 147 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 148 through 164 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 165 through 219 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -3 through 25 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 35 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 36 through 95 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 96 through 140 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 141 through 157 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 158 through 192 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 193 through 219 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -3 through 26 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 27 through 50 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 51 through 121 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 122 through 144 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 145 through 157 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 158 through 219 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid -3 through 26 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 27 through 106 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 107 through 140 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 141 through 157 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 158 through 192 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 193 through 219 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid -3 through 26 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 27 through 50 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 51 through 119 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 120 through 151 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 152 through 164 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 165 through 219 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid -4 through 26 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 27 through 106 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 107 through 121 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 122 through 143 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 144 through 156 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 157 through 192 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 193 through 219 )

-
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