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- PDB-6gqf: The structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol -

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Basic information

Entry
Database: PDB / ID: 6gqf
TitleThe structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol
ComponentsGRAM domain-containing protein 1A
KeywordsLIPID TRANSPORT / cholesterol / plasma membrane / endoplasmic reticulum
Function / homology
Function and homology information


: / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / cholesterol transfer activity / cellular response to cholesterol / cholesterol binding / autophagosome / extrinsic component of cytoplasmic side of plasma membrane / autophagy / cytoplasmic vesicle ...: / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / cholesterol transfer activity / cellular response to cholesterol / cholesterol binding / autophagosome / extrinsic component of cytoplasmic side of plasma membrane / autophagy / cytoplasmic vesicle / membrane => GO:0016020 / endoplasmic reticulum membrane / plasma membrane / cytosol
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
25-HYDROXYCHOLESTEROL / Protein Aster-A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFairall, L. / Gurnett, J.E. / Vashi, D. / Sandhu, J. / Tontonoz, P. / Schwabe, J.W.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustWT100237 United Kingdom
Royal SocietyWolfson Research Merit award United Kingdom
CitationJournal: Cell / Year: 2018
Title: Aster Proteins Facilitate Nonvesicular Plasma Membrane to ER Cholesterol Transport in Mammalian Cells.
Authors: Sandhu, J. / Li, S. / Fairall, L. / Pfisterer, S.G. / Gurnett, J.E. / Xiao, X. / Weston, T.A. / Vashi, D. / Ferrari, A. / Orozco, J.L. / Hartman, C.L. / Strugatsky, D. / Lee, S.D. / He, C. / ...Authors: Sandhu, J. / Li, S. / Fairall, L. / Pfisterer, S.G. / Gurnett, J.E. / Xiao, X. / Weston, T.A. / Vashi, D. / Ferrari, A. / Orozco, J.L. / Hartman, C.L. / Strugatsky, D. / Lee, S.D. / He, C. / Hong, C. / Jiang, H. / Bentolila, L.A. / Gatta, A.T. / Levine, T.P. / Ferng, A. / Lee, R. / Ford, D.A. / Young, S.G. / Ikonen, E. / Schwabe, J.W.R. / Tontonoz, P.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRAM domain-containing protein 1A
B: GRAM domain-containing protein 1A
C: GRAM domain-containing protein 1A
D: GRAM domain-containing protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,96112
Polymers103,9824
Non-polymers1,9798
Water0
1
A: GRAM domain-containing protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4903
Polymers25,9951
Non-polymers4952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GRAM domain-containing protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4903
Polymers25,9951
Non-polymers4952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GRAM domain-containing protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4903
Polymers25,9951
Non-polymers4952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GRAM domain-containing protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4903
Polymers25,9951
Non-polymers4952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.435, 121.012, 71.907
Angle α, β, γ (deg.)90.00, 110.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GRAM domain-containing protein 1A


Mass: 25995.459 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gramd1a, D7Bwg0611e, Kiaa1533 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q8VEF1
#2: Chemical
ChemComp-HC3 / 25-HYDROXYCHOLESTEROL / (3BETA)-CHOLEST-5-ENE-3,25-DIOL


Mass: 402.653 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M NaCl, 0.1 M sodium cacodylate pH6, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→67.203 Å / Num. obs: 18439 / % possible obs: 99 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.033 / Rrim(I) all: 0.105 / Net I/σ(I): 13.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2958 / CC1/2: 0.891 / Rpim(I) all: 0.21 / Rrim(I) all: 0.662 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5yqj

5yqj


Resolution: 2.9→67.203 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 844 4.58 %Random selection
Rwork0.2013 ---
obs0.2039 18413 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→67.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 140 0 5466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045596
X-RAY DIFFRACTIONf_angle_d0.7827593
X-RAY DIFFRACTIONf_dihedral_angle_d11.1142039
X-RAY DIFFRACTIONf_chiral_restr0.034844
X-RAY DIFFRACTIONf_plane_restr0.003938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.08180.31491640.2592878X-RAY DIFFRACTION99
3.0818-3.31980.32981380.2342903X-RAY DIFFRACTION99
3.3198-3.65380.29511110.22342943X-RAY DIFFRACTION99
3.6538-4.18250.29311330.20652922X-RAY DIFFRACTION99
4.1825-5.26910.21581420.17612967X-RAY DIFFRACTION99
5.2691-67.22110.24161560.19332956X-RAY DIFFRACTION99

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