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- PDB-7azn: Structure of mouse AsterC (GramD1c) with a new cholesterol-derive... -

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Basic information

Entry
Database: PDB / ID: 7azn
TitleStructure of mouse AsterC (GramD1c) with a new cholesterol-derived compound
ComponentsProtein Aster-C
KeywordsLIPID TRANSPORT / Non vesicular cholesterol transport / lipid-binding / endoplasmic reticulum / membrane contact sites
Function / homology
Function and homology information


endoplasmic reticulum-plasma membrane contact site / cellular response to cholesterol / cholesterol transfer activity / cholesterol binding / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
VASt domain / VAD1 Analog of StAR-related lipid transfer domain / VASt domain profile. / : / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / PH-like domain superfamily
Similarity search - Domain/homology
ETHANOL / 20alpha-hydroxy-20-(5-methylhexyl)cholesterol / Protein Aster-C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRomartinez-Alonso, B. / Sirvydis, K. / Kim, Y. / Xiao, X. / Jung, M. / Tontonoz, P. / Schwabe, J.
Funding support France, 1items
OrganizationGrant numberCountry
Leducq FoundationTransatlantic Networks of Excellence for Cardiovascular and Neurovascular Research France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Selective Aster inhibitors distinguish vesicular and nonvesicular sterol transport mechanisms.
Authors: Xiao, X. / Kim, Y. / Romartinez-Alonso, B. / Sirvydis, K. / Ory, D.S. / Schwabe, J.W.R. / Jung, M.E. / Tontonoz, P.
History
DepositionNov 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Protein Aster-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6199
Polymers20,8341
Non-polymers7858
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, NBD-Cholesterol Binding experiments and competition assays were performed to obtain the dissociation constant for this compound.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint20 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.995, 49.397, 61.691
Angle α, β, γ (deg.)90.000, 100.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein Aster-C / GRAM domain-containing protein 1C


Mass: 20833.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gramd1c / Plasmid: pGEX / Details (production host): Bacteria expression plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8CI52
#2: Chemical ChemComp-YK8 / 20alpha-hydroxy-20-(5-methylhexyl)cholesterol


Mass: 416.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: A single 100-micrometres rectangular prism.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M SPG buffer pH 4 25 % PEG 1500

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2019 / Details: Mirrors
RadiationMonochromator: Double crystal monochromator 28.900 m / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.09→26.77 Å / Num. obs: 11465 / % possible obs: 97.9 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.057 / Rrim(I) all: 0.083 / Χ2: 0.69 / Net I/σ(I): 7.1
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 808 / CC1/2: 0.944 / Rpim(I) all: 0.239 / Rrim(I) all: 0.347 / Χ2: 0.65 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gqf

6gqf


Resolution: 2.09→26.77 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 580 5.07 %
Rwork0.2172 10868 -
obs0.2193 11448 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.05 Å2 / Biso mean: 41.7578 Å2 / Biso min: 16.36 Å2
Refinement stepCycle: final / Resolution: 2.09→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 54 50 1562
Biso mean--37.19 44.78 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.30.34311430.29432582272594
2.3-2.630.3291500.247327542904100
2.63-3.310.25381490.236927632912100
3.31-26.770.2241380.1872769290797

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