PDB-7w2e: An open-like conformation of the sigma-1 receptor from Xenopus laevis

ID or keywords:

Entry

Database: PDB / ID: 7w2e

Title

An open-like conformation of the sigma-1 receptor from Xenopus laevis

Components

Sigma non-opioid intracellular receptor 1

Keywords

MEMBRANE PROTEIN / sigma receptor / membrane receptor / S1R / ligand entry

Function / homology

Function and homology information

nuclear inner membrane / lipid transport / nuclear outer membrane / 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 /

molecular replacement / Resolution: 3.557 Å

Authors

Meng, F. / Sun, Z. / Zhou, X.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway.
Authors: Meng, F. / Xiao, Y. / Ji, Y. / Sun, Z. / Zhou, X.

History

Deposition	Nov 23, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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	7w2e.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb7w2e.ent.gz	885.9 KB	Display	PDB format
PDBx/mmJSON format	7w2e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7w2e_validation.pdf.gz	504.1 KB	Display	wwPDB validaton report
Full document	7w2e_full_validation.pdf.gz	522.3 KB	Display
Data in XML	7w2e_validation.xml.gz	85.2 KB	Display
Data in CIF	7w2e_validation.cif.gz	112.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w2/7w2e ftp://data.pdbj.org/pub/pdb/validation_reports/w2/7w2e	HTTPS FTP

-
Related structure data

Related structure data	7w2bC 7w2cC 7w2dC 7w2fC 7w2gC 7w2hC 5hk1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7w2e-2 7w2e-3 7w2e-4 3ziy-1 7w2b-2 5jyf-d 5obo-1 6fja-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
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

G: Sigma non-opioid intracellular receptor 1

H: Sigma non-opioid intracellular receptor 1

I: Sigma non-opioid intracellular receptor 1

J: Sigma non-opioid intracellular receptor 1

K: Sigma non-opioid intracellular receptor 1

L: Sigma non-opioid intracellular receptor 1

301 kDa, 12 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
75.4 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
75.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Sigma non-opioid intracellular receptor 1

H: Sigma non-opioid intracellular receptor 1

I: Sigma non-opioid intracellular receptor 1

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

4

J: Sigma non-opioid intracellular receptor 1

K: Sigma non-opioid intracellular receptor 1

L: Sigma non-opioid intracellular receptor 1

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

Unit cell

Length a, b, c (Å)	135.125, 161.466, 200.249
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	(chain A and resid 2 through 219)
2	1	(chain B and resid 2 through 219)
3	1	(chain C and resid 2 through 219)
4	1	(chain D and resid 2 through 219)
5	1	(chain E and resid 2 through 219)
6	1	(chain F and resid 2 through 219)
7	1	(chain G and resid 2 through 219)
8	1	(chain H and resid 2 through 219)
9	1	(chain I and resid 2 through 219)
10	1	(chain J and resid 2 through 219)
11	1	chain K
12	1	(chain L and resid 2 through 219)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 219 / Label seq-ID: 6 - 223

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	(chain A and resid 2 through 219)	A	A
2	(chain B and resid 2 through 219)	B	B
3	(chain C and resid 2 through 219)	C	C
4	(chain D and resid 2 through 219)	D	D
5	(chain E and resid 2 through 219)	E	E
6	(chain F and resid 2 through 219)	F	F
7	(chain G and resid 2 through 219)	G	G
8	(chain H and resid 2 through 219)	H	H
9	(chain I and resid 2 through 219)	I	I
10	(chain J and resid 2 through 219)	J	J
11	chain K	K	K
12	(chain L and resid 2 through 219)	L	L

#1: Protein	Sigma non-opioid intracellular receptor 1 / Sigma 1-type opioid receptor / Sigma1-receptor / Sigma1R Mass: 25121.682 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: sigmar1, oprs1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q6DCU6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.62 Å³/Da / Density % sol: 66.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Na+-HEPES pH 6.5, 28% PEG 300

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.9793 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 3.557→20.01 Å / Num. obs: 51558 / % possible obs: 97.4 % / Redundancy: 4.6 % / B_iso Wilson estimate: 95.19 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.069 / R_rim(I) all: 0.158 / Net I/σ(I): 7.7 / Num. measured all: 235149

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
3.557-3.618	4.6	0.754	11776	2562	0.822	0.367	0.843	1.8	98.2
9.334-20.01	4.3	0.033	11342	2655	0.999	0.017	0.038	24.1	94.4

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XDS	BUILT 20200417	data reduction
Aimless	0.7.4	data scaling
PHASER		phasing
PHENIX	1.13_2998	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HK1

5hk1

Resolution: 3.557→20.01 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2974	2504	4.87 %
R_work	0.264	48914	-
obs	0.2656	51418	97.1 %

Solvent computation

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

Displacement parameters

B_iso max: 202.1 Å² / B_iso mean: 101.3199 Å² / B_iso min: 50.04 Å²

Refinement step

Cycle: final / Resolution: 3.557→20.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20959	0	0	15	20974
B_iso mean	-	-	-	76.8	-
Num. residues	-	-	-	-	2663

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	2	B	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	3	C	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	4	D	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	5	E	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	6	F	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	7	G	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	8	H	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	9	I	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	10	J	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	11	K	12298	X-RAY DIFFRACTION	4.847	TORSIONAL
1	12	L	12298	X-RAY DIFFRACTION	4.847	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.557-3.6249	0.3203	131	0.323	2689	98
3.6249-3.6985	0.3313	151	0.2964	2706	98
3.6985-3.7784	0.2893	121	0.2917	2723	98
3.7784-3.8657	0.2582	142	0.2881	2689	98
3.8657-3.9616	0.3215	136	0.2802	2726	98
3.9616-4.0679	0.3212	127	0.2855	2701	98
4.0679-4.1865	0.296	121	0.2674	2722	98
4.1865-4.3203	0.2876	149	0.2584	2726	98
4.3203-4.4731	0.2662	128	0.2524	2735	98
4.4731-4.65	0.2651	163	0.2427	2678	97
4.65-4.8588	0.2923	139	0.2422	2742	98
4.8588-5.1109	0.2814	151	0.2522	2681	97
5.1109-5.4251	0.2986	143	0.2727	2730	97
5.4251-5.8344	0.3426	148	0.3017	2721	97
5.8344-6.404	0.3889	140	0.2971	2731	97
6.404-7.2911	0.3355	135	0.2621	2748	97
7.2911-9.0427	0.2915	146	0.2195	2735	96
9.0427-20.01	0.2588	133	0.2469	2731	92

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	3.4834	4.1594	-1.456	2.0614	1.527	2.6093	0.4048	0.1832	-0.3212	1.7867	0.4247	-1.3069	0.1197	-0.16	-0.8068	0.9012	-0.1031	-0.207	1.0321	0.1161	0.7114	-13.4324	-4.6077	50.8568
2	2.7416	1.2715	-0.0354	4.1265	-0.8311	0.8716	0.5122	-0.4973	0.2691	0.0613	-0.1082	-0.0949	0.4427	0.296	-0.2966	0.7731	-0.0205	-0.1102	0.903	0.06	0.7611	-36.0237	-39.2067	41.4459
3	3.0606	-0.0455	-0.6293	3.9874	-1.3821	2.2483	0.1485	-0.0974	0.3172	-0.1259	0.204	-0.0379	0.3898	-0.2607	-0.4021	0.6477	-0.0468	-0.0342	0.8232	-0.0223	0.6165	-32.2997	-28.7995	33.0127
4	1.6476	0.8551	0.9357	2.7162	3.6131	4.6908	0.0261	-0.5045	-0.0109	0.7359	-0.2383	0.659	-0.0732	0.1986	0.2068	0.6476	-0.0056	0.1588	0.694	-0.0611	0.5352	-39.9122	-18.5863	42.1068
5	3.3228	1.9475	-0.921	2.3666	-0.1316	3.2814	-0.8208	0.5832	0.6964	0.2759	0.6414	-0.2601	-0.2713	0.1853	-0.0238	0.9628	0.6998	-0.0148	0.8782	-0.1878	1.0906	-60.385	0.3649	41.8212
6	6.4611	0.0341	0.637	0.4577	0.2682	5.6	0.4672	-0.4332	0.5494	-0.388	-0.1843	-0.1851	-0.2693	-0.1491	-0.2073	0.8638	0.0093	-0.1119	0.529	0.058	0.4941	-54.1737	-10.2741	5.2277
7	1.4936	1.3098	0.0018	1.8321	-1.7639	2.1701	0.0696	-0.394	-0.3072	0.072	0.082	0.3048	0.0926	-0.4739	-0.1012	0.7115	0.0328	-0.024	0.8491	0.1208	0.6775	-48.6396	-21.0568	18.3229
8	3.1613	0.0628	1.6967	1.3282	1.0795	0.8116	0.1749	0.1259	0.3138	-0.3541	-0.1278	0.2706	-0.0768	-0.2071	-0.0635	0.8786	-0.0294	-0.0554	0.8501	0.1538	0.5729	-49.1988	-8.6922	13.8448
9	1.9335	0.1738	-0.3125	3.5648	-0.6974	-0.7177	0.3321	-0.172	0.4997	-1.2702	-0.1532	-0.381	0.0995	0.2976	-0.1239	1.3444	-0.2034	0.0692	0.8472	0.1357	0.9442	-19.7813	5.4553	7.924
10	3.5136	-1.0028	-0.9954	2.9679	-0.8331	5.1901	0.0376	-0.4823	0.4943	-0.2735	-0.188	-0.5417	0.0331	0.4808	0.1134	0.7986	-0.1852	0.1891	0.8123	0.2121	0.7561	-13.7192	-15.2073	12.5371
11	1.016	0.6083	0.3385	3.8154	-1.5119	0.6361	0.0448	0.2201	0.1466	-1.2452	0.3265	-1.3161	-0.1639	-0.0021	-0.2112	1.1926	0.0834	0.2289	0.8242	-0.0411	0.6971	-25.6978	-15.6942	4.812
12	0.6226	0.1503	0.4942	3.4889	0.7821	0.6831	0.0206	-0.3961	0.2299	-0.2174	0.059	-0.5617	-0.5203	0.2204	0.0393	0.8242	-0.1679	0.1037	0.7175	0.0654	0.9514	-13.8428	-6.7279	21.6997
13	3.1766	3.0239	1.2467	6.3745	2.7316	3.1575	0.19	-0.6963	-0.3436	-0.9664	-0.3052	-0.1222	-0.1866	-0.6916	0.4009	0.9389	0.1542	0.0021	1.2281	0.0003	0.8623	-53.7508	42.7477	51.1277
14	3.9111	-0.4733	-1.2171	4.0782	3.8618	2.7199	-0.0163	-0.2271	0.2745	-0.0214	0.4241	-0.7266	0.1688	0.1215	-0.3929	0.8364	-0.0579	0.0132	0.8171	-0.098	0.8769	-29.0202	73.8404	40.7258
15	1.5598	-1.3081	1.3241	5.6932	0.9501	2.1874	-0.087	-0.54	0.2042	0.456	0.1225	-0.2349	-0.0975	-0.5243	0.0205	0.7264	-0.0332	-0.0448	0.8142	-0.058	0.8075	-34.3755	63.874	34.5443
16	3.1735	0.1384	-1.2217	3.392	-1.3362	8.1497	-1.2283	0.4222	-1.1098	0.866	-0.8442	-1.2146	-1.1029	0.0681	1.7279	0.6655	0.3368	-0.1305	1.2188	0.1056	1.2076	-6.5339	38.6547	40.1279
17	2.2292	-0.6509	0.5546	1.5355	0.3959	2.5987	-0.0522	-0.1076	0.2738	-0.8894	1.5739	-0.7347	-1.0273	0.4736	-1.054	1.8159	-0.244	0.4465	1.1484	0.2766	1.3835	-6.1975	53.7946	5.6893
18	5.4215	1.0319	-1.51	1.0899	0.7706	1.4042	1.2585	0.2945	1.4035	-0.6905	-0.4985	-1.0025	-0.3723	-0.1259	-0.7182	1.3275	0.2158	0.2252	1.1251	0.0452	0.8548	-16.2515	46.8491	4.2818
19	3.7872	-1.5368	-2.4824	1.2514	2.324	3.6215	0.381	-0.3327	-0.2509	-0.5503	0.1572	-0.5194	-0.092	0.4241	-0.622	0.6531	-0.018	0.0003	0.7707	-0.1021	1.0938	-19.022	59.513	17.8237
20	0.6138	-0.6051	1.2796	1.84	0.4821	3.6955	-0.0941	0.5032	-0.2413	0.003	0.3254	0.7044	-0.2647	0.7409	-0.1446	1.1952	0.0064	0.1844	0.9354	0.0274	1.1194	-16.1757	58.3273	13.9365
21	2.2704	-0.0079	-2.4853	2.2178	0.7688	3.5303	-0.6884	0.612	1.6964	0.4983	0.484	0.0369	0.902	0.3646	0.4585	0.8458	0.0799	-0.1758	0.7997	-0.046	0.9951	-26.7486	43.8643	19.5676
22	4.2787	-1.0832	-0.4896	1.571	-1.7523	2.227	-0.3552	-1.1363	0.0037	-1.0537	0.1118	-0.2521	0.4904	0.6324	0.1226	1.091	0.14	0.0171	0.9999	-0.1748	1.1038	-15.9134	34.9546	8.7343
23	6.8125	-1.2068	0.3035	5.2112	0.3616	1.399	0.7333	-0.757	-0.4226	-2.1857	-0.3986	-0.6583	0.5963	-0.0164	-0.3001	1.1099	-0.2004	0.0292	0.7939	-0.2642	1.197	-40.1574	18.5212	12.7066
24	6.8246	2.1448	-1.2007	4.0337	1.3238	1.7387	0.2028	2.4202	-2.2044	-0.8453	0.6271	-0.9405	0.5939	-1.3816	-0.7279	1.933	0.1093	-0.4988	1.4228	-0.1706	0.8731	-57.9486	51.7001	1.4184
25	1.0311	1.1326	1.2163	2.8255	1.3661	1.3269	0.3542	-0.0028	0.0051	-0.5664	-0.2553	0.3813	0.235	0.0087	-0.0831	1.0108	0.0303	-0.2966	1.0295	-0.1242	1.0891	-57.4394	54.0091	13.5353
26	1.098	-1.1743	-1.4571	1.1306	0.7258	1.9685	-0.0131	0.331	-0.0217	-0.6478	-0.0356	0.1666	0.4781	0.1618	0.1859	1.2056	0.0833	-0.2227	1.1122	-0.1546	0.8506	-40.1333	52.7425	6.3937
27	3.6537	-0.2341	0.1853	1.4785	0.6228	0.735	0.1724	0.4619	0.4158	-1.2117	-1.0307	0.746	-0.9055	0.3381	0.9053	1.5415	0.2463	-0.215	1.0511	-0.0013	1.0654	-44.9312	53.5915	5.3265
28	2.3361	2.0868	-0.8314	1.7166	-0.2035	0.6157	0.009	0.7281	0.6024	-0.3014	0.1873	0.4742	0.1163	-0.1572	-0.1719	1.086	-0.0126	-0.3097	1.0501	-0.0203	1.0594	-53.6487	44.8977	21.6123
29	3.5704	0.7058	0.9679	3.861	0.6085	4.6086	-0.7639	0.52	1.0904	-0.691	1.0064	0.7205	-0.2964	0.598	-0.2711	1.2492	-0.0917	-0.0398	0.8578	0.2562	0.5146	-60.4884	37.1001	40.4658
30	3.0733	-0.7933	-1.2176	3.0104	-0.6512	3.5073	0.1035	0.5522	-0.0385	-0.5192	-0.1428	-0.0545	0.4106	-0.1286	0.0093	0.8013	-0.0227	-0.1241	0.9276	0.0008	0.6664	-87.3488	12.9439	53.0555
31	3.3858	2.4966	1.2221	1.6654	0.9396	1.9185	0.0879	0.2031	0.5589	-0.1705	0.1714	0.3426	-0.2526	-0.2625	-0.1395	0.8262	0.0815	-0.1184	0.7253	-0.0361	0.9444	-83.2294	23.9683	63.3815
32	1.2039	0.9373	-0.7946	0.7702	0.0699	2.6585	-0.2339	1.0451	-0.3264	-0.2826	0.4287	-0.4426	-0.5385	0.3918	-0.2745	0.891	0.0127	-0.0476	1.015	-0.2524	0.7177	-72.8761	11.3736	50.3329
33	1.1369	0.6905	1.4671	0.2021	0.5937	1.5386	0.3427	-0.1537	-0.0278	-0.4177	-0.3098	0.6163	2.3146	1.6095	-0.4257	1.4192	0.6644	0.0063	0.9974	-0.1109	1.391	-53.2088	-8.481	52.8045
34	3.4532	-0.3692	0.1533	2.6968	0.1297	4.4747	-0.0353	-0.7911	-0.3354	0.5967	0.176	-0.2404	0.2905	0.1472	-0.1062	1.0819	-0.002	-0.2489	0.7974	-0.0259	0.6892	-62.3426	-1.9349	86.9665
35	0.2482	0.6436	0.449	2.1203	-1.3124	1.9968	0.324	-0.0034	-0.6417	-0.2376	-0.2499	-0.1614	0.0906	-0.0347	-0.1534	0.9253	-0.0055	-0.2346	0.8501	-0.071	0.7177	-73.9229	3.2592	74.3652
36	2.205	-0.9638	1.7178	0.8803	-0.744	1.1708	-0.045	1.0274	0.3348	0.6245	-0.0153	-0.1721	1.1299	-0.0372	0.2358	0.9317	-0.0594	-0.0625	0.8153	-0.0804	0.6495	-72.4554	0.4797	78.2125
37	1.5713	-1.3463	-0.5103	4.5984	1.7343	4.0905	0.1432	-0.1205	0.0878	-0.2294	-0.3668	-0.463	0.5972	-0.0731	0.1541	0.5446	-0.0248	-0.0778	0.934	-0.1149	0.614	-52.5848	4.8419	78.1561
38	8.5397	-4.9518	-4.6385	8.0533	0.8234	5.5995	-0.0652	-2.4343	-1.5882	-1.8714	0.1191	0.0174	-1.6637	1.1326	-0.1155	0.6703	-0.2818	-0.1946	1.1619	0.0461	1.2052	-33.1159	26.0465	77.7353
39	5.1797	1.3048	0.0187	5.8625	-2.2515	6.657	0.1684	-0.3465	-0.7501	1.4374	-0.0607	-1.1428	0.5433	-1.4376	-0.2753	1.1888	-0.0104	-0.2347	1.2645	-0.4124	1.0445	-67.0156	42.5855	89.9674
40	2.1613	0.5012	-1.6688	1.8715	0.4701	1.0427	0.4562	0.3783	0.3691	0.9183	-0.0584	0.0807	0.0378	0.3356	-0.4297	0.8142	0.0523	-0.146	0.6413	-0.1375	1.1651	-70.8129	44.6754	78.1016
41	0.1222	-1.1076	0.8274	3.0112	-1.1727	3.0242	-0.0129	0.1246	0.0867	0.2401	-0.1396	-0.693	0.1475	0.4081	0.1808	0.6082	-0.0657	-0.1014	0.7511	-0.1351	0.9602	-66.119	29.0208	81.3935
42	2.0878	-1.1038	-0.199	0.6107	0.3038	0.1478	0.219	0.1978	0.8673	-0.345	0.131	-0.4729	-0.2281	0.8638	-0.3321	0.713	-0.3055	0.1497	0.8159	-0.0601	1.0236	-59.4817	44.9326	69.9208
43	3.055	1.2457	1.2265	2.5769	0.6822	2.378	0.6135	-1.1024	0.3739	0.0323	-0.2032	-0.0946	-0.1109	0.1196	-0.4109	0.8491	-0.101	0.046	0.9211	-0.1724	0.8837	-7.2271	0.8865	40.1689
44	3.0197	2.1427	0.8163	3.4138	1.6693	2.3437	-0.186	-0.0015	-0.5238	-0.5785	0.5367	-0.6296	0.3586	0.1448	-0.3247	0.9	-0.0483	0.0229	0.942	-0.1362	1.0305	26.3876	23.4119	52.1572
45	3.1279	-0.0714	-0.3949	3.1468	-1.2879	1.6206	0.1069	-0.2253	-0.3211	0.1345	-0.2121	0.0035	0.0038	0.2173	0.0944	0.6134	-0.0318	0.0099	0.7791	0.0082	0.704	15.3291	19.1753	59.5517
46	2.7805	0.3196	2.0355	2.9348	-0.4609	2.7274	-0.0661	0.1771	-0.2623	-0.0648	-0.3684	-0.1211	-0.1027	-0.2422	0.4196	0.6472	-0.0185	-0.1177	0.8606	0.1193	0.6901	5.64	26.9018	50.0179
47	2.197	1.9447	-0.0647	2.5818	2.0019	5.1136	0.2145	0.0027	1.7944	0.556	-2.6976	1.2255	-0.5886	-0.8139	1.0106	0.8226	1.0222	-0.4359	1.0531	0.3581	1.1154	-13.8976	47.1296	53.5196
48	1.1974	-0.5309	-0.0272	2.9038	-0.8955	3.3076	0.4183	-0.3182	0.4611	0.3421	-0.1088	0.2957	-0.5863	-0.1284	-0.2458	1.0103	-0.0649	0.2018	0.9682	-0.0681	0.9079	-4.9811	40.3846	87.6284
49	-0.1184	-0.0493	-0.0651	0.6383	0.9518	2.0894	-0.299	0.4887	0.1741	-0.2419	0.1443	0.1049	-0.4439	0.5075	0.1485	0.9229	-0.1106	0.118	1.0704	0.1154	1.2043	-0.9306	36.7353	77.3552
50	0.7567	-0.9622	-0.3494	1.5256	1.6328	3.5046	-0.4758	-0.4542	0.6607	0.2642	0.0399	0.6758	-0.2022	0.1677	0.2595	0.9064	-0.1536	0.0689	0.8171	-0.1581	1.0573	11.9774	36.8146	75.3875
51	2.3301	-1.9107	0.0328	1.4983	-0.968	3.048	0.2591	-0.0283	-0.5855	0.4726	-0.0656	0.6592	-0.8308	0.7824	-0.3316	0.8632	-0.2241	0.1339	1.1645	-0.1015	1.0201	2.1623	36.9877	77.0209
52	3.3034	-2.6668	1.9497	3.17	-1.8789	5.3536	0.0878	0.0911	-0.7062	-0.0491	-0.4076	0.3807	-0.39	-0.8829	0.1662	0.6787	-0.0401	0.0992	0.8396	0.1397	0.9392	-14.8491	33.4467	77.7563
53	0.1849	-0.457	0.8111	6.6849	0.7382	0.8112	-0.9859	-0.0072	-0.2425	-0.7565	0.2651	-2.4799	0.6762	-0.6408	0.0974	0.7629	-0.3012	0.3578	1.4584	0.0577	-0.1166	-33.8333	11.9553	78.1495
54	7.1663	1.8757	2.397	3.6001	0.9767	5.1602	0.7547	-0.4516	-0.7187	1.6035	-0.2755	-0.0972	0.4941	-0.223	-0.2483	1.2386	0.1672	0.0792	1.0691	0.2572	1.4824	-0.451	-4.1554	89.7744
55	1.692	-0.2551	0.3971	1.1681	-0.708	2.3395	0.1326	-0.0614	-1.0404	-0.0894	0.292	0.3896	0.5623	-0.1353	-0.2853	0.9399	-0.1161	0.0967	1.0139	0.2986	1.5779	3.5805	-6.3125	77.9698
56	1.6599	0.9105	0.3676	0.5691	-1.023	1.711	-0.0397	-0.4971	-0.2669	0.1943	0.0425	0.1503	-0.0765	-0.1061	-0.1512	0.9398	-0.1239	0.1835	1.0229	0.2203	1.1715	-1.2455	9.3214	81.1012
57	0.9083	1.0872	0.9511	1.5234	0.5398	1.2657	0.2613	-0.179	-1.556	0.1953	0.1166	-0.6487	0.9081	-1.6851	-0.2302	0.7882	-0.2077	0.0165	0.9569	0.0857	1.4341	-7.7002	-6.6811	69.6543

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 28 )	A	-3 - 28
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 65 )	A	29 - 65
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 174 )	A	66 - 174
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 175 through 219 )	A	175 - 219
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -3 through 29 )	B	-3 - 29
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 30 through 106 )	B	30 - 106
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 140 )	B	107 - 140
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 141 through 219 )	B	141 - 219
9	X-RAY DIFFRACTION	9	chain 'C' and (resid -3 through 50 )	C	-3 - 50
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 51 through 127 )	C	51 - 127
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 128 through 174 )	C	128 - 174
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 175 through 219 )	C	175 - 219
13	X-RAY DIFFRACTION	13	chain 'D' and (resid -3 through 28 )	D	-3 - 28
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 29 through 85 )	D	29 - 85
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 86 through 219 )	D	86 - 219
16	X-RAY DIFFRACTION	16	chain 'E' and (resid -1 through 29 )	E	-1 - 29
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 30 through 50 )	E	30 - 50
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 51 through 106 )	E	51 - 106
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 107 through 140 )	E	107 - 140
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 141 through 174 )	E	141 - 174
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 175 through 192 )	E	175 - 192
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 193 through 219 )	E	193 - 219
23	X-RAY DIFFRACTION	23	chain 'F' and (resid -3 through 28 )	F	-3 - 28
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 29 through 50 )	F	29 - 50
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 51 through 106 )	F	51 - 106
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 107 through 140 )	F	107 - 140
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 141 through 174 )	F	141 - 174
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 175 through 219 )	F	175 - 219
29	X-RAY DIFFRACTION	29	chain 'G' and (resid -2 through 29 )	G	-2 - 29
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 30 through 106 )	G	30 - 106
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 107 through 174 )	G	107 - 174
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 175 through 219 )	G	175 - 219
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 1 through 29 )	H	1 - 29
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 30 through 106 )	H	30 - 106
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 107 through 140 )	H	107 - 140
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 141 through 174 )	H	141 - 174
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 175 through 219 )	H	175 - 219
38	X-RAY DIFFRACTION	38	chain 'I' and (resid -3 through 29 )	I	-3 - 29
39	X-RAY DIFFRACTION	39	chain 'I' and (resid 30 through 50 )	I	30 - 50
40	X-RAY DIFFRACTION	40	chain 'I' and (resid 51 through 85 )	I	51 - 85
41	X-RAY DIFFRACTION	41	chain 'I' and (resid 86 through 192 )	I	86 - 192
42	X-RAY DIFFRACTION	42	chain 'I' and (resid 193 through 219 )	I	193 - 219
43	X-RAY DIFFRACTION	43	chain 'J' and (resid -3 through 29 )	J	-3 - 29
44	X-RAY DIFFRACTION	44	chain 'J' and (resid 30 through 65 )	J	30 - 65
45	X-RAY DIFFRACTION	45	chain 'J' and (resid 66 through 174 )	J	66 - 174
46	X-RAY DIFFRACTION	46	chain 'J' and (resid 175 through 219 )	J	175 - 219
47	X-RAY DIFFRACTION	47	chain 'K' and (resid 2 through 29 )	K	2 - 29
48	X-RAY DIFFRACTION	48	chain 'K' and (resid 30 through 95 )	K	30 - 95
49	X-RAY DIFFRACTION	49	chain 'K' and (resid 96 through 127 )	K	96 - 127
50	X-RAY DIFFRACTION	50	chain 'K' and (resid 128 through 151 )	K	128 - 151
51	X-RAY DIFFRACTION	51	chain 'K' and (resid 152 through 174 )	K	152 - 174
52	X-RAY DIFFRACTION	52	chain 'K' and (resid 175 through 219 )	K	175 - 219
53	X-RAY DIFFRACTION	53	chain 'L' and (resid -2 through 29 )	L	-2 - 29
54	X-RAY DIFFRACTION	54	chain 'L' and (resid 30 through 50 )	L	30 - 50
55	X-RAY DIFFRACTION	55	chain 'L' and (resid 51 through 85 )	L	51 - 85
56	X-RAY DIFFRACTION	56	chain 'L' and (resid 86 through 192 )	L	86 - 192
57	X-RAY DIFFRACTION	57	chain 'L' and (resid 193 through 219 )	L	193 - 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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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