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- PDB-5yqi: Crystal structure of the first StARkin domain of Lam2 -

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Basic information

Entry
Database: PDB / ID: 5yqi
TitleCrystal structure of the first StARkin domain of Lam2
ComponentsMembrane-anchored lipid-binding protein YSP2
KeywordsTRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport
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 / apoptotic process / endoplasmic reticulum membrane ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / sterol transport / cortical endoplasmic reticulum / 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
Membrane-anchored lipid-binding protein YSP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTong, J. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
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 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
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


Theoretical massNumber of molelcules
Total (without water)19,2451
Polymers19,2451
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8910 Å2
Unit cell
Length a, b, c (Å)33.433, 59.505, 84.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 19244.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pHis2-Thr
Details (production host): an N-terminal hexa-histidine tag fusion
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06681
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES-NaOH pH 6.0, 30% PEG3350, 0.1M KNO3

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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: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 22632 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 45.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1117 / % possible all: 100

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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: 5YQJ

5yqj


Resolution: 1.6→23.973 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1122 4.97 %Random selection
Rwork0.206 ---
obs0.2078 22588 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 0 119 1447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061355
X-RAY DIFFRACTIONf_angle_d0.7461836
X-RAY DIFFRACTIONf_dihedral_angle_d14.208820
X-RAY DIFFRACTIONf_chiral_restr0.053214
X-RAY DIFFRACTIONf_plane_restr0.005226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.599-1.67180.24551300.22282623X-RAY DIFFRACTION98
1.6718-1.75990.25081680.21422657X-RAY DIFFRACTION100
1.7599-1.87010.23951390.21922681X-RAY DIFFRACTION100
1.8701-2.01450.24671570.20472667X-RAY DIFFRACTION100
2.0145-2.21710.22941500.22706X-RAY DIFFRACTION100
2.2171-2.53760.28131370.21212718X-RAY DIFFRACTION100
2.5376-3.19590.23631280.20872763X-RAY DIFFRACTION100
3.1959-23.97540.24261130.19972651X-RAY DIFFRACTION91

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