+Open data
-Basic information
Entry | Database: PDB / ID: 1n6h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Rab5a | ||||||
Components | Ras-related protein Rab-5A | ||||||
Keywords | PROTEIN TRANSPORT / Rab / GTPase | ||||||
Function / homology | Function and homology information regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of autophagosome assembly / regulation of filopodium assembly / RAB geranylgeranylation / early endosome to late endosome transport ...regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of autophagosome assembly / regulation of filopodium assembly / RAB geranylgeranylation / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / canonical Wnt signaling pathway / endomembrane system / axon terminus / phagocytic vesicle / phagocytosis / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / ruffle / small monomeric GTPase / G protein activity / clathrin-coated endocytic vesicle membrane / regulation of long-term neuronal synaptic plasticity / intracellular protein transport / terminal bouton / receptor internalization / endocytosis / phagocytic vesicle membrane / GDP binding / melanosome / synaptic vesicle / actin cytoskeleton / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / early endosome / endosome membrane / endosome / membrane raft / axon / intracellular membrane-bounded organelle / GTPase activity / dendrite / neuronal cell body / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.51 Å | ||||||
Authors | Zhu, G. / Liu, J. / Terzyan, S. / Zhai, P. / Li, G. / Zhang, X.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: High Resolution Crystal Structures of Human Rab5a and Five Mutants with Substitutions in the Catalytically Important Phosphate-Binding Loop Authors: Zhu, G. / Liu, J. / Terzyan, S. / Zhai, P. / Li, G. / Zhang, X.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n6h.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n6h.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 1n6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n6h ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n6h | HTTPS FTP |
---|
-Related structure data
Related structure data | 1n6iC 1n6kC 1n6lC 1n6nC 1n6oC 1n6pC 1n6rC 1huqS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18987.572 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20339 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: Chemical | ChemComp-BME / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 23, 2002 |
Radiation | Monochromator: OSMIC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→20 Å / Num. all: 24442 / Num. obs: 24259 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 1.51→1.56 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.2 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 24442 / % possible obs: 99.5 % / Num. measured all: 134293 |
Reflection shell | *PLUS % possible obs: 99.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1HUQ Resolution: 1.51→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.176 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|