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- PDB-4afi: Complex between Vamp7 longin domain and fragment of delta-adaptin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4afi | ||||||
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Title | Complex between Vamp7 longin domain and fragment of delta-adaptin from AP3 | ||||||
![]() | AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 | ||||||
![]() | ENDOCYTOSIS / EXOCYTOSIS / CLATHRIN ADAPTOR / CHIMERA / FUSION PROTEIN | ||||||
Function / homology | ![]() synaptic vesicle budding from endosome / : / presynaptic endosome / anterograde synaptic vesicle transport / regulation of protein targeting to vacuolar membrane / synaptic vesicle membrane organization / AP-3 adaptor complex / triglyceride transport / vesicle fusion with Golgi apparatus / endosome to melanosome transport ...synaptic vesicle budding from endosome / : / presynaptic endosome / anterograde synaptic vesicle transport / regulation of protein targeting to vacuolar membrane / synaptic vesicle membrane organization / AP-3 adaptor complex / triglyceride transport / vesicle fusion with Golgi apparatus / endosome to melanosome transport / neutrophil degranulation / Golgi to vacuole transport / eosinophil degranulation / positive regulation of NK T cell differentiation / vesicle fusion / vesicle transport along microtubule / SNARE complex / SNAP receptor activity / neurotransmitter receptor transport, postsynaptic endosome to lysosome / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / calcium-ion regulated exocytosis / protein targeting to vacuole / Golgi to plasma membrane protein transport / melanosome organization / protein localization to membrane / anterograde axonal transport / positive regulation of dendrite morphogenesis / SNARE complex assembly / syntaxin binding / phagocytosis, engulfment / endosome to lysosome transport / exocytosis / pseudopodium / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / transport vesicle / axon cytoplasm / phagocytic vesicle / hippocampal mossy fiber to CA3 synapse / SNARE binding / filopodium / intracellular protein transport / terminal bouton / synaptic vesicle membrane / phagocytic vesicle membrane / synaptic vesicle / apical part of cell / lamellipodium / late endosome membrane / postsynapse / endosome membrane / neuron projection / lysosomal membrane / Golgi membrane / glutamatergic synapse / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kent, H.M. / Evans, P.R. / Luzio, J.P. / Peden, A.A. / Owen, D.J. | ||||||
![]() | ![]() Title: Structural Basis of the Intracellular Sorting of the Snare Vamp7 by the Ap3 Adaptor Complex Authors: Kent, H.M. / Evans, P.R. / Schaefer, I.B. / Gray, S.R. / Sanderson, C.M. / Luzio, J.P. / Peden, A.A. / Owen, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vx8S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.766, 0.632, 0.12), Vector: |
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Components
#1: Protein | Mass: 19556.240 Da / Num. of mol.: 2 Fragment: DELTA-ADAPTIN HINGE, RESIDUES 680-729, VAMP7 LONGIN DOMAIN, RESIDUES 1-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: PGEX4T2 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % Description: SIGNIFICANT ANISOTROPY IN DATA. SECOND DATA SET AT 1.5 ANGSTROM UNITS. COLLECTED TO ENHANCE ANOMALOUS DATA FROM PR3+ IONS. |
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Crystal grow | pH: 9 Details: 4 M NACL, 100 MM BICINE PH 9.0, 10 MM PRASEODYMIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→64 Å / Num. obs: 11810 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.9 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VX8 Resolution: 2.8→61.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.216 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.863 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. NCS APPLIED AS LOCAL RESTRAINTS WITH ADDITIONAL TARGET OF PREVIOUS VAMP7 STRUCTURE.
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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 mean: 60.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→61.01 Å
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Refine LS restraints |
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