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- PDB-8w4b: The sigma-1 receptor from Xenopus laevis in complex with progeste... -

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Basic information

Entry
Database: PDB / ID: 8w4b
TitleThe sigma-1 receptor from Xenopus laevis in complex with progesterone by co-crystallization
ComponentsSigma non-opioid intracellular receptor 1
KeywordsMEMBRANE PROTEIN / sigma receptor / S1R / endogenous ligand / neurosteroid / P4
Function / homology
Function and homology information


ergosterol biosynthetic process / nuclear outer membrane / nuclear inner membrane / lipid transport / cytoplasmic vesicle / endoplasmic reticulum membrane / 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: 2.152 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

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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
Water1,35175
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 area12510 Å2
ΔGint-69 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.196, 161.196, 161.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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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 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 63.75 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.105→43.081 Å / Num. obs: 20044 / % possible obs: 95.5 % / Redundancy: 23 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.027 / Rrim(I) all: 0.129 / Net I/σ(I): 14.6 / Num. measured all: 460385
Reflection shellResolution: 2.105→2.148 Å / % possible obs: 83.4 % / Redundancy: 18.4 % / Rmerge(I) obs: 2.747 / Num. measured all: 17995 / Num. unique obs: 980 / Rpim(I) all: 0.656 / Rrim(I) all: 2.825 / Net I/σ(I) obs: 1.1

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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: 2.152→32.904 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 915 4.83 %
Rwork0.1984 --
obs0.1993 18962 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.152→32.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 23 75 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041839
X-RAY DIFFRACTIONf_angle_d0.7842504
X-RAY DIFFRACTIONf_dihedral_angle_d14.2571039
X-RAY DIFFRACTIONf_chiral_restr0.047285
X-RAY DIFFRACTIONf_plane_restr0.004304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.152-2.26520.30331160.26322293X-RAY DIFFRACTION87
2.2652-2.40710.25111150.22372654X-RAY DIFFRACTION100
2.4071-2.59290.22891370.20562624X-RAY DIFFRACTION100
2.5929-2.85360.2151220.21342474X-RAY DIFFRACTION93
2.8536-3.26630.22951230.20942679X-RAY DIFFRACTION100
3.2663-4.11390.21571410.18972502X-RAY DIFFRACTION93
4.1139-32.9040.19671610.18832821X-RAY DIFFRACTION100
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)
13.3724-1.4962-0.36818.5173-5.55345.21680.04810.1232-0.1529-0.2438-0.16430.01970.28660.04620.14920.4272-0.01070.00070.4118-0.09230.3148-14.5862-50.15789.8412
21.1183-0.5517-0.18580.21810.28841.7256-0.0089-0.1319-0.16760.05140.029-0.02440.0810.1002-0.05050.4056-0.02340.02710.35130.03970.3955-16.7271-37.334824.4415
35.2132-4.6905-0.66364.54130.74193.3205-0.5029-0.204-1.37950.84190.19930.8610.35330.12850.30160.4655-0.09140.04440.39410.0920.7234-25.0594-55.559520.0921
49.6096-7.2222-7.95995.81617.12789.6451-0.5473-0.1629-0.1911.55670.10030.23980.90660.20550.54970.6278-0.09560.05920.50040.14470.4437-23.7118-35.995751.9088
55.2217-0.965-1.06062.031-0.85928.44-0.0475-0.1963-0.60820.2978-0.0785-0.14460.42411.21910.1780.4290.0118-0.04790.4761-0.04380.5542-6.5152-47.294619.5103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 219 )
4X-RAY DIFFRACTION4chain 'A' and (resid -5 through 26 )
5X-RAY DIFFRACTION5chain 'A' and (resid 27 through 50 )

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