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- PDB-8hs7: Crystal structure of Vesicle-associated membrane protein-associat... -

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Basic information

Entry
Database: PDB / ID: 8hs7
TitleCrystal structure of Vesicle-associated membrane protein-associated protein SCS2 from yeast
ComponentsVesicle-associated membrane protein-associated protein SCS2
KeywordsCELL ADHESION
Function / homology
Function and homology information


endoplasmic reticulum polarization / regulation of intracellular lipid transport / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / RHOC GTPase cycle / endoplasmic reticulum membrane organization / endoplasmic reticulum inheritance / regulation of phosphatidylinositol dephosphorylation / nucleus-vacuole junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane ...endoplasmic reticulum polarization / regulation of intracellular lipid transport / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / RHOC GTPase cycle / endoplasmic reticulum membrane organization / endoplasmic reticulum inheritance / regulation of phosphatidylinositol dephosphorylation / nucleus-vacuole junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cellular bud tip / phospholipid biosynthetic process / cellular bud neck / reticulophagy / negative regulation of protein import into nucleus / subtelomeric heterochromatin formation / protein-membrane adaptor activity / 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
Chem-EDT / Vesicle-associated membrane protein-associated protein SCS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal structure of the major sperm protein domain of SCS2 from saccharomyces cerevisiae
Authors: Xu, T.
History
DepositionDec 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2252
Polymers13,9331
Non-polymers2921
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.689, 68.689, 56.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

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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: 13932.947 Da / Num. of mol.: 1 / Fragment: MSP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCS2, YER120W / Production host: Escherichia coli (E. coli) / References: UniProt: P40075
#2: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1 mM tris-bis (pH 5.5). 0.1 M EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10680 / % possible obs: 99.81 % / Redundancy: 19 % / Biso Wilson estimate: 39.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05229 / Rpim(I) all: 0.01233 / Net I/σ(I): 37.12
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.6431 / Mean I/σ(I) obs: 4.49 / Num. unique obs: 1312 / CC1/2: 0.95 / Rpim(I) all: 0.1588

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Processing

Software
NameVersionClassification
PHENIXdev_4778refinement
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.92 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2606 1058 9.91 %
Rwork0.2495 9622 -
obs0.2505 10680 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.45 Å2
Refinement stepCycle: LAST / Resolution: 2→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 20 47 1047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341019
X-RAY DIFFRACTIONf_angle_d0.62751384
X-RAY DIFFRACTIONf_chiral_restr0.0473161
X-RAY DIFFRACTIONf_plane_restr0.0034176
X-RAY DIFFRACTIONf_dihedral_angle_d17.8156381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.34631320.33531180X-RAY DIFFRACTION98.94
2.09-2.20.28911290.29631172X-RAY DIFFRACTION99.85
2.2-2.340.30351310.3051182X-RAY DIFFRACTION99.77
2.34-2.520.3341280.29721192X-RAY DIFFRACTION99.92
2.52-2.770.29921320.28931194X-RAY DIFFRACTION100
2.77-3.170.27361350.27361205X-RAY DIFFRACTION100
3.18-40.26351340.22731220X-RAY DIFFRACTION100
4-40.920.21451370.21681277X-RAY DIFFRACTION100

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