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- PDB-8w4c: The sigma-1 receptor from Xenopus laevis in complex with progeste... -

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Basic information

Entry
Database: PDB / ID: 8w4c
TitleThe sigma-1 receptor from Xenopus laevis in complex with progesterone by soaking
ComponentsSigma non-opioid intracellular receptor 1
KeywordsMEMBRANE 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
ERG2/sigma1 receptor-like / ERG2 and Sigma1 receptor like protein
Similarity search - Domain/homology
PROGESTERONE / Sigma non-opioid intracellular receptor 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.676 Å
AuthorsXiao, Y. / Fu, C. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: 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
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sigma non-opioid intracellular receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0352
Polymers25,7201
Non-polymers3141
Water46826
1
A: Sigma non-opioid intracellular receptor 1
hetero molecules

A: Sigma non-opioid intracellular receptor 1
hetero molecules

A: Sigma non-opioid intracellular receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1046
Polymers77,1613
Non-polymers9433
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area12650 Å2
ΔGint-66 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.226, 161.226, 161.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

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Components

#1: Protein Sigma non-opioid intracellular receptor 1


Mass: 25720.322 Da / Num. of mol.: 1
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: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 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, 1mM progesterone soaking

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→38.001 Å / Num. obs: 11200 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Net I/σ(I): 8.2 / Num. measured all: 74720
Reflection shellResolution: 2.6→2.65 Å / % possible obs: 92.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.583 / Num. measured all: 3757 / Num. unique obs: 549 / Rpim(I) all: 0.646 / Rrim(I) all: 1.713 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
XDSBUILT 20220820data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.676→38.001 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 523 5.03 %
Rwork0.2172 --
obs0.2184 10395 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.676→38.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 23 26 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041839
X-RAY DIFFRACTIONf_angle_d0.7362504
X-RAY DIFFRACTIONf_dihedral_angle_d13.8731039
X-RAY DIFFRACTIONf_chiral_restr0.044285
X-RAY DIFFRACTIONf_plane_restr0.003304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.676-2.94520.31621270.27712414X-RAY DIFFRACTION100
2.9452-3.37110.29411260.25022431X-RAY DIFFRACTION100
3.3711-4.24640.2081310.2142468X-RAY DIFFRACTION100
4.2464-38.0010.22461390.19442559X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.3102-0.05450.23110.0144-0.02260.1746-0.30430.0063-0.26010.64070.17860.21950.4567-0.026-0.00010.8174-0.09690.18760.450.03280.5076-23.6732-36.008551.9243
20.7178-0.38970.15970.4191-0.40081.1904-0.1474-0.0005-0.13480.08770.059-0.04320.01130.1730.00010.407-0.01770.00290.4285-0.01740.4561-12.5995-47.498714.9646
30.3744-0.5376-0.42810.76980.51690.6217-0.0044-0.1247-0.03830.10980.0873-0.0705-0.06620.175400.4073-0.01690.02820.37750.0580.3634-16.0414-37.329224.8387
40.24820.0560.360.08680.10840.5296-0.36650.0319-0.02710.41430.0790.24870.1027-0.2808-0.11110.486-0.06110.10970.29480.0810.4619-25.0205-55.565320.1529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 192 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 219 )

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