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- PDB-8hqu: Crystal structure of the major sperm protein domain of SCS2 from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hqu | ||||||
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Title | Crystal structure of the major sperm protein domain of SCS2 from saccharomyces cerevisiae | ||||||
![]() | Vesicle-associated membrane protein-associated protein SCS2 | ||||||
![]() | CELL ADHESION / MSP (Major sperm protein) domain | ||||||
Function / homology | ![]() endoplasmic reticulum polarization / regulation of intracellular lipid transport / endoplasmic reticulum membrane organization / RHOC GTPase cycle / 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 ...endoplasmic reticulum polarization / regulation of intracellular lipid transport / endoplasmic reticulum membrane organization / RHOC GTPase cycle / 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 / reticulophagy / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the major sperm protein domain of SCS2 from saccharomyces cerevisiae Authors: Xu, T. / Wang, C.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.6 KB | Display | ![]() |
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PDB format | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15124.235 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SCS2, YER120W / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1 mM tris-bis (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 10613 / % possible obs: 99.88 % / Redundancy: 19.3 % / Biso Wilson estimate: 38.34 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0766 / Rpim(I) all: 0.0179 / Rrim(I) all: 0.0787 / Net I/σ(I): 28.32 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.9656 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 2607 / CC1/2: 0.94 / CC star: 0.98 / Rpim(I) all: 0.2236 / Rrim(I) all: 0.9915 / % possible all: 99.81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold Resolution: 2→40.81 Å / SU ML: 0.2243 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.9958 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.69 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.81 Å
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Refine LS restraints |
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LS refinement shell |
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