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- PDB-6lp4: Structural basis and functional analysis epo1-bem3p complex for b... -

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Basic information

Entry
Database: PDB / ID: 6lp4
TitleStructural basis and functional analysis epo1-bem3p complex for bud growth
ComponentsVesicle-associated membrane protein-associated protein SCS2
KeywordsCELL ADHESION / Budding yeast / Organelle inheritance / Endoplasmic reticulum inheritance / Polarisome / X-ray crystallography
Function / homology
Function and homology information


endoplasmic reticulum polarization / regulation of intracellular lipid transport / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum inheritance / nucleus-vacuole junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cellular bud tip ...endoplasmic reticulum polarization / regulation of intracellular lipid transport / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum inheritance / nucleus-vacuole junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cellular bud tip / phospholipid biosynthetic process / cellular bud neck / negative regulation of protein import into nucleus / subtelomeric heterochromatin formation / Neutrophil degranulation / phosphatidylinositol binding / nuclear envelope / nuclear membrane / chromosome, telomeric region / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Vesicle-associated membrane protein-associated protein SCS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.049 Å
AuthorsWang, J.
CitationJournal: To Be Published
Title: Structural basis and functional analysis epo1-bem3p complex for bud growth
Authors: Wang, J.
History
DepositionJan 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Vesicle-associated membrane protein-associated protein SCS2


Theoretical massNumber of molelcules
Total (without water)14,1511
Polymers14,1511
Non-polymers00
Water0
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 area7490 Å2
Unit cell
Length a, b, c (Å)70.660, 70.660, 56.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Vesicle-associated membrane protein-associated protein SCS2 / VAMP-associated protein SCS2 / Choline sensitivity suppressor protein 2 / VAP homolog 1


Mass: 14151.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SCS2, YER120W / Production host: Escherichia coli (E. coli) / References: UniProt: P40075

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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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium sulfate, 0.1 M Bis-Tris, pH 8.0, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10060 / % possible obs: 99.9 % / Redundancy: 18 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.13 Å / Rmerge(I) obs: 0.084 / Num. unique obs: 9897

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.049→41.528 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.31
RfactorNum. reflection% reflection
Rfree0.2813 537 5.34 %
Rwork0.2602 --
obs0.2614 10060 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.54 Å2 / Biso mean: 42.3306 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.049→41.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 0 980
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0492-2.25540.3961040.3465202282
2.2554-2.58180.34811520.3111242199
2.5818-3.25260.27391290.29192498100
3.2526-41.5280.25121520.22472582100

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