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- PDB-1w6k: Structure of human OSC in complex with Lanosterol -

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Basic information

Entry
Database: PDB / ID: 1w6k
TitleStructure of human OSC in complex with Lanosterol
ComponentsLANOSTEROL SYNTHASE
KeywordsISOMERASE / CYCLASE / CHOLESTEROL / LANOSTEROL / MONOTOPIC MEMBRANE PROTEIN / B-OCTYL-GLUCOSIDE / STEROID BIOSYNTHESIS
Function / homology
Function and homology information


lanosterol synthase / lanosterol synthase activity / triterpenoid biosynthetic process / Cholesterol biosynthesis / steroid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / lipid droplet / Activation of gene expression by SREBF (SREBP) / regulation of protein stability ...lanosterol synthase / lanosterol synthase activity / triterpenoid biosynthetic process / Cholesterol biosynthesis / steroid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / lipid droplet / Activation of gene expression by SREBF (SREBP) / regulation of protein stability / endoplasmic reticulum membrane / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase and squalene oxidase repeat ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Special / Mainly Alpha
Similarity search - Domain/homology
LANOSTEROL / Lanosterol synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsThoma, R. / Schulz-Gasch, T. / D'Arcy, B. / Benz, J. / Aebi, J. / Dehmlow, H. / Hennig, M. / Ruf, A.
Citation
Journal: Nature / Year: 2004
Title: Insight Into Steroid Scaffold Formation from the Structure of Human Oxidosqualene Cyclase
Authors: Thoma, R. / Schulz-Gasch, T. / D'Arcy, B. / Benz, J. / Aebi, J. / Dehmlow, H. / Hennig, M. / Stihle, M. / Ruf, A.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: The Monotopic Membrane Protein Human Osc is Active as Monomer
Authors: Ruf, A. / Muller, F. / D'Arcy, B. / Stihle, M. / Kuznir, E. / Handschin, C. / Morand, O. / Thoma, R.
History
DepositionAug 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LANOSTEROL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,15810
Polymers83,3931
Non-polymers2,7669
Water17,348963
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)189.570, 201.472, 62.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LANOSTEROL SYNTHASE / OXIDOSQUALENE--LANOSTEROL CYCLASE / OXIDO SQUALENE CYCLASE / 2 / 3-EPOXYSQUALENE--LANOSTEROL CYCLASE / OSC


Mass: 83392.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P48449, lanosterol synthase
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-LAN / LANOSTEROL


Mass: 426.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: (S)-2,3-EPOXYSQUALENE = LANOSTEROL.

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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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growDetails: 25% (W/V) PEG3350 0.4M AMMONIUM ACETATE 0.1M TRIS PH 8.5 10% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 79898 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 96.3

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Processing

Software
NameClassification
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.188 -5 %RANDOM
Rwork0.147 ---
obs-0 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5816 0 116 963 6895

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