+Open data
-Basic information
Entry | Database: PDB / ID: 1n6o | ||||||
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Title | Crystal Structure of Human Rab5a A30K mutant complex with GppNHp | ||||||
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 / RAB geranylgeranylation / regulation of filopodium assembly / early endosome to late endosome transport / regulation of autophagosome assembly ...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 / RAB geranylgeranylation / regulation of filopodium assembly / early endosome to late endosome transport / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / early phagosome / Respiratory syncytial virus (RSV) attachment and entry / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / canonical Wnt signaling pathway / endomembrane system / phagocytosis / axon terminus / phagocytic vesicle / ruffle / Prevention of phagosomal-lysosomal fusion / somatodendritic compartment / small monomeric GTPase / G protein activity / clathrin-coated endocytic vesicle membrane / intracellular protein transport / regulation of long-term neuronal synaptic plasticity / terminal bouton / receptor internalization / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / GDP binding / Clathrin-mediated endocytosis / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / melanosome / synaptic vesicle / early endosome membrane / endosome / endosome membrane / early endosome / membrane raft / axon / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / dendrite / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n6o.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n6o.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n6o_validation.pdf.gz | 728.6 KB | Display | wwPDB validaton report |
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Full document | 1n6o_full_validation.pdf.gz | 729.5 KB | Display | |
Data in XML | 1n6o_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1n6o_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n6o ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n6o | HTTPS FTP |
-Related structure data
Related structure data | 1n6hC 1n6iC 1n6kC 1n6lC 1n6nC 1n6pC 1n6rC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19045.674 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN / Mutation: A30K 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 |
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#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 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 16, 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: 1.8→20 Å / Num. all: 14404 / Num. obs: 13961 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.3 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 14404 / % possible obs: 99.7 % / Num. measured all: 83171 |
Reflection shell | *PLUS % possible obs: 99.3 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 14667 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.174 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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