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- PDB-5ys0: Crystal structure of the second StARkin domain of Lam2 in complex... -

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Basic information

Entry
Database: PDB / ID: 5ys0
TitleCrystal structure of the second StARkin domain of Lam2 in complex with ergosterol
ComponentsMembrane-anchored lipid-binding protein YSP2
KeywordsTRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport / Ysp2
Function / homology
Function and homology information


intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / sterol transport / cortical endoplasmic reticulum / cell periphery / mitochondrial membrane / endoplasmic reticulum membrane / apoptotic process ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / sterol transport / cortical endoplasmic reticulum / cell periphery / mitochondrial membrane / endoplasmic reticulum membrane / apoptotic process / 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 / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsTong, J. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4004914 Korea, Republic Of
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites
Authors: Tong, J. / Manik, M.K. / Im, Y.J.
History
DepositionNov 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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: Membrane-anchored lipid-binding protein YSP2
B: Membrane-anchored lipid-binding protein YSP2
C: Membrane-anchored lipid-binding protein YSP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1955
Polymers57,4013
Non-polymers7932
Water37821
1
A: Membrane-anchored lipid-binding protein YSP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5302
Polymers19,1341
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane-anchored lipid-binding protein YSP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5302
Polymers19,1341
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Membrane-anchored lipid-binding protein YSP2


Theoretical massNumber of molelcules
Total (without water)19,1341
Polymers19,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.717, 70.315, 42.508
Angle α, β, γ (deg.)90.00, 103.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Membrane-anchored lipid-binding protein YSP2 / 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: 19133.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YSP2, LAM2, LTC4, YDR326C / Plasmid: pHIS2-Thr
Details (production host): N-terminal hexahistidine tag fusion
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3) / References: UniProt: Q06681
#2: Chemical ChemComp-ERG / ERGOSTEROL


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl pH 8.0, 30% PEG8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16717 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 48.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 845 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YQJ

4yqj


Resolution: 2.601→32.709 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 799 4.79 %random selection
Rwork0.241 ---
obs0.2436 16685 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→32.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 58 21 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013910
X-RAY DIFFRACTIONf_angle_d1.1655296
X-RAY DIFFRACTIONf_dihedral_angle_d21.5131566
X-RAY DIFFRACTIONf_chiral_restr0.071620
X-RAY DIFFRACTIONf_plane_restr0.01652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.7640.3771330.31412621X-RAY DIFFRACTION99
2.764-2.97730.41931380.33622651X-RAY DIFFRACTION99
2.9773-3.27660.30331210.29972689X-RAY DIFFRACTION100
3.2766-3.75020.31961450.25052644X-RAY DIFFRACTION100
3.7502-4.72260.28431220.21742703X-RAY DIFFRACTION100
4.7226-32.71170.24621400.20662578X-RAY DIFFRACTION95

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