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- PDB-3mjh: Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Fi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mjh | ||||||
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Title | Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 | ||||||
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![]() | PROTEIN TRANSPORT / PROTEIN-ZINC FINGER COMPLEX / BETA BETA ALPHA FOLD / BETA HAIRPIN / Rab5A GTPase / EEA1 | ||||||
Function / homology | ![]() serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / chemical synaptic transmission, postsynaptic / synaptic vesicle recycling / axonal spine ...serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / chemical synaptic transmission, postsynaptic / synaptic vesicle recycling / axonal spine / amyloid-beta clearance by transcytosis / modulation by host of viral process / vesicle fusion / GTP-dependent protein binding / 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 / Respiratory syncytial virus (RSV) attachment and entry / canonical Wnt signaling pathway / endomembrane system / phagocytosis / axon terminus / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / ruffle / phagocytic vesicle / small monomeric GTPase / G protein activity / intracellular protein transport / regulation of long-term neuronal synaptic plasticity / clathrin-coated endocytic vesicle membrane / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / recycling endosome / endocytosis / phagocytic vesicle membrane / GDP binding / melanosome / actin cytoskeleton / synaptic vesicle / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / postsynapse / early endosome / endosome membrane / calmodulin binding / endosome / membrane raft / axon / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / glutamatergic synapse / dendrite / GTP binding / Golgi apparatus / protein homodimerization activity / zinc ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mishra, A.K. / Eathiraj, S. / Lambright, D.G. | ||||||
![]() | ![]() Title: Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1). Authors: Mishra, A. / Eathiraj, S. / Corvera, S. / Lambright, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.5 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 999.6 KB | Display | ![]() |
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Full document | ![]() | 1003.8 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein | Mass: 18801.445 Da / Num. of mol.: 2 / Fragment: residues 16-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain (production host): K12, BL21 (DE3)Codon Plus RIL cells References: UniProt: P20339, small monomeric GTPase #2: Protein/peptide | Mass: 3678.005 Da / Num. of mol.: 2 / Fragment: C2H2-type, residues 36-69 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain (production host): K12, BL21(DE3)Codon Plus RIL cells References: UniProt: Q15075 |
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-Non-polymers , 4 types, 318 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2007 / Details: mirrors |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 27931 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 35.344 Å2 / Rsym value: 0.042 / Net I/σ(I): 44.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: mouse Rab5C Resolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.351 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.275 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.193 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.025→2.077 Å / Total num. of bins used: 20
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