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Open data
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Basic information
Entry | Database: PDB / ID: 1n6n | ||||||
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Title | Crystal Structure of Human Rab5a A30R mutant complex with GppNHp | ||||||
![]() | Ras-related protein Rab-5A | ||||||
![]() | PROTEIN TRANSPORT / Rab / GTPase | ||||||
Function / homology | ![]() 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 / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / intracellular protein transport / regulation of long-term neuronal synaptic plasticity / clathrin-coated endocytic vesicle membrane / terminal bouton / receptor internalization / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / GDP binding / actin cytoskeleton / melanosome / synaptic vesicle / 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 / neuronal cell body / dendrite / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, G. / Liu, J. / Terzyan, S. / Zhai, P. / Li, G. / Zhang, X.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.7 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1n6hC ![]() 1n6iC ![]() 1n6kC ![]() 1n6lC ![]() 1n6oC ![]() 1n6pC ![]() 1n6rC C: citing same article ( |
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Similar structure data |
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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: 19073.688 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN / Mutation: A30R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 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: 1.6→20 Å / Num. all: 20607 / Num. obs: 19898 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 20607 / % possible obs: 99.7 % / Num. measured all: 88810 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→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 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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