+Open data
-Basic information
Entry | Database: PDB / ID: 3g2s | ||||||
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Title | VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ADP-ribosylation factor binding protein GGA1 / VHS / acidic-cluster dileucine signal / SorLA | ||||||
Function / homology | Function and homology information positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / protein localization to ciliary membrane / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / adaptive thermogenesis / post-Golgi vesicle-mediated transport ...positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / protein localization to ciliary membrane / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / adaptive thermogenesis / post-Golgi vesicle-mediated transport / protein retention in Golgi apparatus / endosome to plasma membrane protein transport / low-density lipoprotein particle receptor activity / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / Golgi to plasma membrane protein transport / low-density lipoprotein particle binding / positive regulation of protein exit from endoplasmic reticulum / negative regulation of amyloid precursor protein catabolic process / protein targeting to lysosome / Golgi to plasma membrane transport / multivesicular body membrane / neuropeptide binding / aspartic-type endopeptidase inhibitor activity / regulation of smooth muscle cell migration / protein localization to cell surface / retrograde transport, endosome to Golgi / TBC/RABGAPs / transport vesicle membrane / nuclear envelope lumen / insulin receptor recycling / diet induced thermogenesis / negative regulation of amyloid-beta formation / protein maturation / negative regulation of BMP signaling pathway / neuropeptide signaling pathway / protein targeting / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / positive regulation of adipose tissue development / multivesicular body / phosphatidylinositol binding / receptor-mediated endocytosis / ubiquitin binding / intracellular protein transport / protein catabolic process / trans-Golgi network / protein localization / recycling endosome / small GTPase binding / negative regulation of neurogenesis / recycling endosome membrane / positive regulation of protein catabolic process / cell migration / transmembrane signaling receptor activity / amyloid-beta binding / early endosome membrane / early endosome / endosome membrane / endosome / Amyloid fiber formation / Golgi membrane / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum membrane / Golgi apparatus / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Cramer, J.F. / Behrens, M.A. / Gustafsen, C. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S. | ||||||
Citation | Journal: Traffic / Year: 2010 Title: GGA autoinhibition revisited Authors: Cramer, J.F. / Gustafsen, C. / Behrens, M.A. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g2s.cif.gz | 148.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g2s.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 3g2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/3g2s ftp://data.pdbj.org/pub/pdb/validation_reports/g2/3g2s | HTTPS FTP |
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-Related structure data
Related structure data | 3g2tC 3g2uC 3g2vC 3g2wC 1jwfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16958.564 Da / Num. of mol.: 2 / Fragment: VHS Domain (N-terminal domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: UniProt: Q9UJY5 #2: Protein/peptide | Mass: 1364.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q92673 #3: Chemical | ChemComp-HEZ / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2007 |
Radiation | Monochromator: high resolution Si(311) cut and a lower resolution Si(111) cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 34624 / Num. obs: 34575 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.21 % / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 8.26 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.81 / Num. unique all: 5312 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JWF Resolution: 1.7→49.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU B: 4.283 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / ESU R: 0.119 / ESU R Free: 0.113 / Phase error: 20.12 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.098 Å2 / ksol: 0.339 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.7 Å2 / Biso mean: 19.96 Å2 / Biso min: 5.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→49.33 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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