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- PDB-1tu3: Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tu3 | ||||||
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Title | Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain | ||||||
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![]() | PROTEIN TRANSPORT / Rab5 / Rabaptin5 / effector-binding | ||||||
Function / homology | ![]() regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / RAB geranylgeranylation / Golgi to plasma membrane transport / regulation of filopodium assembly ...regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / RAB geranylgeranylation / Golgi to plasma membrane transport / 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 / endocytic vesicle / canonical Wnt signaling pathway / endomembrane system / phagocytosis / axon terminus / vesicle-mediated transport / phagocytic vesicle / ruffle / Prevention of phagosomal-lysosomal fusion / somatodendritic compartment / GTPase activator activity / small monomeric GTPase / G protein activity / intracellular protein transport / growth factor activity / regulation of long-term neuronal synaptic plasticity / clathrin-coated endocytic vesicle membrane / terminal bouton / recycling endosome / receptor internalization / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / GDP binding / actin cytoskeleton / melanosome / protein transport / synaptic vesicle / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / membrane fusion / early endosome / endosome membrane / endosome / membrane raft / protein domain specific binding / axon / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / dendrite / GTP binding / apoptotic process / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C. | ||||||
![]() | ![]() Title: Structural basis of Rab5-Rabaptin5 interaction in endocytosis Authors: Zhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / 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 | ![]() | 232.1 KB | Display | ![]() |
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PDB format | ![]() | 184.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1tu4C ![]() 1n6hS S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19118.766 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 9076.241 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GNP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 54048 / Num. obs: 54048 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N6H Resolution: 2.31→29.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 423796.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.6721 Å2 / ksol: 0.304902 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→29.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
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Xplor file |
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