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- PDB-6cay: Crystal structure of the first StART-like domain of Ysp2p/Lam2p i... -

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Basic information

Entry
Database: PDB / ID: 6cay
TitleCrystal structure of the first StART-like domain of Ysp2p/Lam2p in its apo and ergosterol-bound state.
ComponentsSterol-binding protein
KeywordsLIPID BINDING PROTEIN / membrane contact sites / lipid transport protein / cholesterol / StART domain / endoplasmic reticulum
Function / homology
Function and homology information


intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / cell periphery / mitochondrial membrane / apoptotic process ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / cell periphery / mitochondrial membrane / apoptotic process / endoplasmic reticulum membrane / mitochondrion / plasma membrane / cytoplasm
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
ERGOSTEROL / : / Membrane-anchored lipid-binding protein YSP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHorenkamp, F.A. / Valverde, D.P. / Reinisch, K.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM80616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM097432 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM106019 United States
CitationJournal: EMBO J. / Year: 2018
Title: Molecular basis for sterol transport by StART-like lipid transfer domains.
Authors: Horenkamp, F.A. / Valverde, D.P. / Nunnari, J. / Reinisch, K.M.
History
DepositionFeb 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterol-binding protein
B: Sterol-binding protein
C: Sterol-binding protein
D: Sterol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4356
Polymers76,6424
Non-polymers7932
Water12,773709
1
A: Sterol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5572
Polymers19,1611
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sterol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5572
Polymers19,1611
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sterol-binding protein


Theoretical massNumber of molelcules
Total (without water)19,1611
Polymers19,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sterol-binding protein


Theoretical massNumber of molelcules
Total (without water)19,1611
Polymers19,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.594, 63.562, 77.540
Angle α, β, γ (deg.)90.00, 103.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sterol-binding protein / Lipid transfer at contact site protein 4 / Lipid transfer protein anchored at membrane contact ...Lipid transfer at contact site protein 4 / Lipid transfer protein anchored at membrane contact sites 3 / Yeast suicide protein 2


Mass: 19160.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YSP2, SCKG_0199 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A250W8A7, UniProt: Q06681*PLUS
#2: Chemical ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H44O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 32.5% PEG 3350, 0.1 M sodium acetate pH 4.9, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→75.4 Å / Num. obs: 42580 / % possible obs: 94.4 % / Redundancy: 20.4 % / Net I/σ(I): 30.4
Reflection shellResolution: 1.89→1.96 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→75.373 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.79
RfactorNum. reflection% reflection
Rfree0.2008 2205 5.18 %
Rwork0.1611 --
obs0.1632 42580 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→75.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5251 0 58 709 6018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075452
X-RAY DIFFRACTIONf_angle_d0.9367416
X-RAY DIFFRACTIONf_dihedral_angle_d9.2112006
X-RAY DIFFRACTIONf_chiral_restr0.062868
X-RAY DIFFRACTIONf_plane_restr0.006906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.22871270.16842500X-RAY DIFFRACTION96
2.0435-2.09110.19391410.16852419X-RAY DIFFRACTION98
2.0911-2.14340.25091270.172527X-RAY DIFFRACTION98
2.1434-2.20130.23141540.16652479X-RAY DIFFRACTION97
2.2013-2.26610.22841290.15852503X-RAY DIFFRACTION97
2.2661-2.33920.2251400.16282482X-RAY DIFFRACTION98
2.3392-2.42280.20331280.1612500X-RAY DIFFRACTION98
2.4228-2.51990.2021160.1612558X-RAY DIFFRACTION98
2.5199-2.63450.20241360.16322514X-RAY DIFFRACTION98
2.6345-2.77350.2151360.1732536X-RAY DIFFRACTION99
2.7735-2.94720.20011360.16662516X-RAY DIFFRACTION98
2.9472-3.17480.19121270.17072568X-RAY DIFFRACTION99
3.1748-3.49430.19521530.15892526X-RAY DIFFRACTION99
3.4943-3.99990.1961670.15632529X-RAY DIFFRACTION99
3.9999-5.03930.14831380.13562582X-RAY DIFFRACTION99
5.0393-75.42650.20681500.17012636X-RAY DIFFRACTION99

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