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Open data
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Basic information
Entry | Database: PDB / ID: 4n3z | ||||||
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Title | Crystal structure of Rabex-5delta and Rabaptin-5C21 complex | ||||||
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![]() | ENDOCYTOSIS / Rab5 / Rabex-5 / Rabaptin-5 / GEF activity / early endosome | ||||||
Function / homology | ![]() dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / negative regulation of mast cell cytokine production / Golgi to plasma membrane transport / RAB GEFs exchange GTP for GDP on RABs / negative regulation of Ras protein signal transduction / TBC/RABGAPs / protein targeting to membrane / mast cell degranulation / negative regulation of interleukin-6 production / endocytic vesicle / vesicle-mediated transport / GTPase activator activity / guanyl-nucleotide exchange factor activity / receptor-mediated endocytosis / negative regulation of protein phosphorylation / growth factor activity / recycling endosome / small GTPase binding / negative regulation of inflammatory response / endocytosis / ubiquitin protein ligase activity / protein transport / early endosome membrane / Ras protein signal transduction / membrane fusion / early endosome / endosome / protein domain specific binding / intracellular membrane-bounded organelle / apoptotic process / dendrite / nucleolus / protein homodimerization activity / protein-containing complex / DNA binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Z. / Zhang, T. / Ding, J. | ||||||
![]() | ![]() Title: Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5 Authors: Zhang, Z. / Zhang, T. / Wang, S. / Gong, Z. / Tang, C. / Chen, J. / Ding, J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.5 KB | Display | ![]() |
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PDB format | ![]() | 136.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459 KB | Display | ![]() |
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Full document | ![]() | 470.3 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n3xC ![]() 4n3yC ![]() 4q9uC ![]() 1txuS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 36564.043 Da / Num. of mol.: 1 / Fragment: UNP residues, isoform 2, 132-455 / Mutation: residues 387-408 deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 10701.068 Da / Num. of mol.: 2 / Fragment: UNP residues 552-642 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | Sequence details | THE REFERENCE SEQUENCE OF CHAIN A IS ISOFORM 2 OF Q9UJ41, AND RESIDUES 387-408 HAVE BEEN DELETED. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0M NaH2PO4/K2HPO4, 0.05% n-octyl-beta-D-galactopyranoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 13730 / % possible obs: 98.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 6 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.4 / Num. unique all: 13730 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TXU Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.763 / Occupancy max: 1 / Occupancy min: 1 / SU B: 49.255 / SU ML: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 230.81 Å2 / Biso mean: 71.9543 Å2 / Biso min: 14.31 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.103→3.184 Å / Total num. of bins used: 20
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