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Yorodumi- PDB-1tu3: Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tu3 | ||||||
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Title | Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Rab5 / Rabaptin5 / effector-binding | ||||||
Function / homology | Function and homology information 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 / 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 / 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 / clathrin-coated endocytic vesicle membrane / intracellular protein transport / growth factor activity / regulation of long-term neuronal synaptic plasticity / terminal bouton / recycling endosome / 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 / protein transport / synaptic vesicle / early endosome membrane / endosome / membrane fusion / endosome membrane / early 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Zhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tu3.cif.gz | 232.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tu3.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tu3_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1tu3_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 1tu3_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 1tu3_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tu3 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tu3 | HTTPS FTP |
-Related structure data
Related structure data | 1tu4C 1n6hS S: Starting model for refinement 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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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.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Plasmid: pET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20339 #2: Protein | Mass: 9076.241 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1, RABPT5, RABPT5A / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15276 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GNP / #5: 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: 2.4 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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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