PDB-8ybb: Crystal structure of the sigma-1 receptor from Xenopus laevis wit...

ID or keywords:

Entry

Database: PDB / ID: 8ybb

Title

Crystal structure of the sigma-1 receptor from Xenopus laevis with side opening

Components

Sigma non-opioid intracellular receptor 1

Keywords

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

Function / homology

Function and homology information

regulation of response to endoplasmic reticulum stress / nuclear inner membrane / nuclear outer membrane / regulation of neuron apoptotic process / nuclear envelope / signaling receptor activity / cytoplasmic vesicle / postsynaptic density / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function

Biological species

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.12 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	Feb 12, 2024	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	8ybb.cif.gz	534.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ybb.ent.gz	449.1 KB	Display	PDB format
PDBx/mmJSON format	8ybb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8w4bC 8w4cC 8w4dC 8w4eC 8wueC 8wwbC 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
Evidence: gel filtration
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
Evidence: gel filtration
77.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.901, 146.848, 145.804
Angle α, β, γ (deg.)	90.00, 107.01, 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

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.33 %
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: BL19U1 / Wavelength: 0.97861 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97861 Å / Relative weight: 1
Reflection	Resolution: 2.808→46.476 Å / Num. obs: 32257 / % possible obs: 75.6 % / Redundancy: 5.6 % / R_merge(I) obs: 0.109 / R_pim(I) all: 0.051 / R_rim(I) all: 0.12 / Net I/σ(I): 10.3 / Num. measured all: 179405
Reflection shell	Resolution: 2.808→3.048 Å / % possible obs: 17.4 % / Redundancy: 5 % / R_merge(I) obs: 1.262 / Num. measured all: 8064 / Num. unique obs: 1613 / R_pim(I) all: 0.628 / R_rim(I) all: 1.413 / Net I/σ(I) obs: 1.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
Aimless	0.7.4	data scaling
XDS	BUILT 20230630	data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.12→44.815 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2671	1501	4.83 %
R_work	0.2354	-	-
obs	0.237	31105	99.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.12→44.815 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10512	0	0	0	10512

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10788
X-RAY DIFFRACTION	f_angle_d	0.491	14658
X-RAY DIFFRACTION	f_dihedral_angle_d	13.094	6132
X-RAY DIFFRACTION	f_chiral_restr	0.037	1668
X-RAY DIFFRACTION	f_plane_restr	0.003	1794

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 (%)
3.12-3.2203	0.4005	142	0.356	2659	X-RAY DIFFRACTION	100
3.2203-3.3353	0.3182	124	0.309	2699	X-RAY DIFFRACTION	100
3.3353-3.4688	0.3105	131	0.2835	2676	X-RAY DIFFRACTION	100
3.4688-3.6266	0.2732	134	0.249	2666	X-RAY DIFFRACTION	100
3.6266-3.8177	0.284	131	0.2444	2698	X-RAY DIFFRACTION	100
3.8177-4.0568	0.2676	140	0.2365	2713	X-RAY DIFFRACTION	100
4.0568-4.3698	0.232	144	0.2246	2654	X-RAY DIFFRACTION	100
4.3698-4.8091	0.2336	141	0.2007	2693	X-RAY DIFFRACTION	100
4.8091-5.5039	0.2682	146	0.2257	2691	X-RAY DIFFRACTION	100
5.5039-6.9302	0.2832	126	0.2779	2717	X-RAY DIFFRACTION	100
6.9302-44.815	0.2559	142	0.2008	2738	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	2.7141	-0.6213	-0.0909	2.2914	-0.3755	4.6797	-0.4842	0.2832	-0.4653	-0.1297	-0.6812	0.4781	1.3841	-0.3955	0.0324	0.7787	0.0016	0.1826	0.996	-0.1497	1.0668	0.816	-27.18	41.88
2	2.0274	-0.1734	-0.4405	1.8911	-0.2448	2.7406	0.3877	0.8941	0.1066	-0.951	-0.5651	0.4679	-0.1488	-0.4318	0.1207	1.0948	0.5108	-0.1209	1.1786	-0.033	0.5726	17.699	-38.256	18.13
3	2.2525	-1.0481	-0.3915	2.2282	0.3908	3.9182	0.2298	0.0975	-0.0121	-0.1859	-0.5077	-1.0975	-1.3011	-0.237	-0.0266	0.8088	0.0102	-0.2253	0.7771	0.0543	0.7573	29.014	-9.069	48.096
4	2.0631	-1.0888	-0.0904	1.6756	-0.648	1.7419	-0.0098	-0.245	-0.2814	0.4408	-0.0696	0.1367	0.0503	-0.166	0.2082	0.9189	0.0532	0.1829	0.9164	0.0592	0.695	13.434	-42.143	56.597
5	1.8246	-1.1155	-0.9421	3.3382	-1.0979	1.4521	0.1374	-0.3143	-0.1199	0.4141	-0.1577	0.0817	-0.2681	-0.2153	0.0961	0.7147	0.1961	-0.0091	0.7846	-0.0151	0.5536	19.473	-35.396	51.072
6	1.7323	1.069	0.3012	1.691	0.6504	1.5159	0.2049	-0.0396	-0.2477	-0.5706	0.0932	-1.0111	-0.5007	-0.1056	-0.163	0.8936	0.2212	0.2342	0.8555	-0.0231	1.0781	40.595	-19.469	33.312
7	1.5429	-0.177	-0.6581	0.6825	0.6089	1.3909	0.6456	0.4636	0.8611	-0.4916	-0.2999	-0.4845	-0.1555	0.2251	-0.2677	0.8346	0.2779	0.1478	0.8778	0.1498	1.2063	39.597	-22.818	34.604
8	3.972	-0.3661	-1.127	3.7923	-0.662	4.3168	0.0604	0.1204	0.1599	0.4045	-0.019	-0.4348	-0.7852	-0.1028	0.1538	0.504	0.0526	-0.1861	0.7445	-0.0981	0.7159	23.389	-0.409	50.583
9	1.928	1.0006	-0.0267	2.4197	-0.6333	1.6339	0.5709	0.7642	0.5117	-0.2526	0.0112	-0.3604	-0.4879	0.0055	-0.2289	1.1358	0.3328	0.27	0.9726	0.1854	0.7885	19.334	21.014	19.673
10	-0.0137	0.1456	-0.1307	1.0104	-0.8822	2.0856	0.1287	0.1628	0.113	0.0359	-0.2938	-0.5606	-0.1141	0.1773	0.1392	0.746	0.2604	0.0748	0.8633	0.0855	0.9559	16.835	15.275	29.039
11	1.642	-0.4249	0.0245	1.1261	-0.3922	2.6702	0.0226	-0.5418	0.5955	0.2063	-0.7474	0.7303	0.6893	-0.6159	0.0255	1.0616	-0.0688	0.023	0.8893	-0.0882	1.0988	-3.711	-17.872	39.547
12	1.3415	0.6991	-0.1259	1.2147	-0.5362	3.7836	-0.1418	-0.4834	-0.216	0.3227	-0.1161	-0.0654	-0.7443	-0.6433	0.163	1.028	0.308	-0.0696	1.0056	-0.0372	0.8468	4.59	12.063	63.816
13	0.7762	-0.8727	0.4299	1.9649	0.8135	1.7923	0.2023	-0.228	-0.4208	0.0202	-0.4232	0.2112	0.4657	-0.0039	0.1861	0.812	0.1881	-0.1048	0.7546	0.0132	0.7241	-2.464	9.094	51.868
14	0.5912	0.0611	-0.4321	1.6145	0.1996	1.0469	-0.1737	-0.0016	0.0229	0.2758	-0.1515	0.2193	-0.1183	0.1605	0.296	0.6972	0.2257	0.0138	0.7253	0.0183	0.7195	7.594	4.485	54.923
15	1.1868	0.0225	-0.3601	2.4886	0.5124	2.6499	0.1896	1.0483	-0.5769	-0.9935	0.3136	0.0262	0.6017	0.9213	-0.3253	1.7185	0.5012	0.1654	1.3205	0.0688	0.7525	18.068	-3.762	17.64
16	1.7893	-0.2319	0.2293	1.8055	0.0903	1.2136	-0.2659	1.2379	-0.301	-1.06	0.3972	0.3953	0.2203	-1.0114	-0.1703	1.5334	0.1756	-0.2413	1.4294	0.0087	1.6173	-18.992	-1.709	18.38
17	1.4681	0.389	0.5796	1.6358	0.1172	2.2145	-0.0368	0.2463	-0.1562	-0.4462	0.0745	0.3993	0.5332	-0.0409	-0.0682	0.9724	0.1346	-0.1288	0.8891	-0.056	1.0217	-15.017	-2.471	29.727
18	1.2363	0.6801	-0.2453	0.4284	-0.4451	1.0514	0.255	0.4176	0.6048	-1.0637	-0.0166	0.7912	-0.2918	-0.4653	-0.1622	0.8377	0.2725	-0.0929	1.0052	0.097	0.8824	-8.589	7.733	22.265
19	2.134	-0.2731	-0.8023	1.7272	-0.334	0.9666	0.0466	0.4081	-0.224	-0.4822	0.019	0.3854	-0.3045	-0.3751	-0.1244	0.9684	0.2366	-0.1431	0.784	-0.0691	0.8921	-8.013	-11.697	32.527

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 -3:26 )	A	-3 - 26
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 27:217 )	A	27 - 217
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID -3:25 )	B	-3 - 25
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 26:106 )	B	26 - 106
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 107:219 )	B	107 - 219
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID -3:95 )	C	-3 - 95
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 96:219 )	C	96 - 219
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID -3:26 )	D	-3 - 26
9	X-RAY DIFFRACTION	9	( CHAIN D AND RESID 27:95 )	D	27 - 95
10	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 96:219 )	D	96 - 219
11	X-RAY DIFFRACTION	11	( CHAIN E AND RESID -3:25 )	E	-3 - 25
12	X-RAY DIFFRACTION	12	( CHAIN E AND RESID 26:85 )	E	26 - 85
13	X-RAY DIFFRACTION	13	( CHAIN E AND RESID 86:147 )	E	86 - 147
14	X-RAY DIFFRACTION	14	( CHAIN E AND RESID 148:219 )	E	148 - 219
15	X-RAY DIFFRACTION	15	( CHAIN F AND RESID -3:26 )	F	-3 - 26
16	X-RAY DIFFRACTION	16	( CHAIN F AND RESID 27:50 )	F	27 - 50
17	X-RAY DIFFRACTION	17	( CHAIN F AND RESID 51:118 )	F	51 - 118
18	X-RAY DIFFRACTION	18	( CHAIN F AND RESID 119:175 )	F	119 - 175
19	X-RAY DIFFRACTION	19	( CHAIN F AND RESID 176:219 )	F	176 - 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