+Open data
-Basic information
Entry | Database: PDB / ID: 7zgb | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of yeast Sec14p with NPPM112 | ||||||
Components | SEC14 cytosolic factor | ||||||
Keywords | LIPID BINDING PROTEIN / Sec14p / NPPM112 | ||||||
Function / homology | Function and homology information negative regulation of phosphatidylcholine biosynthetic process / negative regulation of phosphatidylglycerol biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport ...negative regulation of phosphatidylcholine biosynthetic process / negative regulation of phosphatidylglycerol biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport / Golgi membrane / Golgi apparatus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Hong, Z. / Johnen, P. / Schaaf, G. / Bono, F. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Mechanisms by which small molecules of diverse chemotypes arrest Sec14 lipid transfer activity. Authors: Chen, X.R. / Poudel, L. / Hong, Z. / Johnen, P. / Katti, S. / Tripathi, A. / Nile, A.H. / Green, S.M. / Khan, D. / Schaaf, G. / Bono, F. / Bankaitis, V.A. / Igumenova, T.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7zgb.cif.gz | 136 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zgb.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 7zgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/7zgb ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zgb | HTTPS FTP |
---|
-Related structure data
Related structure data | 7zg9C 7zgaC 7zgcC 7zgdC 1auaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34045.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SEC14, PIT1, YMR079W, YM9582.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P24280 |
---|---|
#2: Chemical | ChemComp-IUJ / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.62 % |
---|---|
Crystal grow | Temperature: 294 K / Method: evaporation Details: 129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol adjusted to pH 7.0 |
-Data collection
Diffraction | Mean temperature: 124 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 23922 / % possible obs: 99.5 % / Redundancy: 3.64 % / Rrim(I) all: 0.142 / Net I/σ(I): 8.29 |
Reflection shell | Resolution: 2.7→7.98 Å / Num. unique obs: 23922 / Rrim(I) all: 0.142 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1aua Resolution: 2.7→20 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 30.85 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 24.7315 Å / Origin y: -27.7328 Å / Origin z: 0.8525 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |