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- PDB-5yqq: Crystal structure of a domain-swapped dimer of the second StARkin... -

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Basic information

Entry
Database: PDB / ID: 5yqq
TitleCrystal structure of a domain-swapped dimer of the second StARkin domain of Lam2
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
Membrane-anchored lipid-binding protein YSP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Membrane-anchored lipid-binding protein YSP2
B: Membrane-anchored lipid-binding protein YSP2


Theoretical massNumber of molelcules
Total (without water)38,2682
Polymers38,2682
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-43 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.862, 52.124, 53.021
Angle α, β, γ (deg.)107.81, 90.17, 105.05
Int Tables number1
Space group name H-MP1

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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.: 2
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): 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.: 223 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl pH 8.0, 30% PEG 8000

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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: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25976 / % possible obs: 97.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 32.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1273 / % possible all: 96.6

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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: 1.9→24.017 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 1284 4.94 %random selection
Rwork0.1937 ---
obs0.196 25975 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 0 223 2760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062583
X-RAY DIFFRACTIONf_angle_d0.8623489
X-RAY DIFFRACTIONf_dihedral_angle_d12.9051559
X-RAY DIFFRACTIONf_chiral_restr0.055406
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8839-1.95930.28691380.21982567X-RAY DIFFRACTION92
1.9593-2.04840.271620.23092719X-RAY DIFFRACTION97
2.0484-2.15640.29931400.22112766X-RAY DIFFRACTION97
2.1564-2.29140.27551790.22342712X-RAY DIFFRACTION97
2.2914-2.46810.25841460.22312791X-RAY DIFFRACTION98
2.4681-2.71620.25961300.22172765X-RAY DIFFRACTION98
2.7162-3.10850.27431440.21462806X-RAY DIFFRACTION98
3.1085-3.91370.21071260.17562815X-RAY DIFFRACTION99
3.9137-24.01850.20431190.16162750X-RAY DIFFRACTION96

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