+Open data
-Basic information
Entry | Database: PDB / ID: 2vx8 | ||||||
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Title | Vamp7 longin domain Hrb peptide complex | ||||||
Components | NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 | ||||||
Keywords | ENDOCYTOSIS / EXOCYTOSIS / MEMBRANE PROTEIN / SIGNAL-ANCHOR / SNARE / MEMBRANE / ENDOSOME / LYSOSOME / TRANSPORT / CYTOPLASMIC VESICLE / ENDOPLASMIC RETICULUM / PROTEIN TRANSPORT / VESICLE TRANSPORT / TRANSMEMBRANE / GOLGI APPARATUS / CLATHRIN ADAPTOR | ||||||
Function / homology | Function and homology information regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / triglyceride transport / natural killer cell degranulation / spermatid nucleus differentiation / vesicle fusion with Golgi apparatus / acrosome assembly / neutrophil degranulation / intermediate filament organization / eosinophil degranulation ...regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / triglyceride transport / natural killer cell degranulation / spermatid nucleus differentiation / vesicle fusion with Golgi apparatus / acrosome assembly / neutrophil degranulation / intermediate filament organization / eosinophil degranulation / vesicle fusion / Golgi to plasma membrane protein transport / vesicle transport along microtubule / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / platelet alpha granule / SNARE complex assembly / positive regulation of dendrite morphogenesis / syntaxin binding / azurophil granule membrane / phagocytosis, engulfment / endosome to lysosome transport / exocytosis / pseudopodium / endoplasmic reticulum to Golgi vesicle-mediated transport / mRNA export from nucleus / phagocytic vesicle / nuclear pore / transport vesicle / vesicle-mediated transport / hippocampal mossy fiber to CA3 synapse / GTPase activator activity / SNARE binding / secretory granule membrane / filopodium / secretory granule / trans-Golgi network / synaptic vesicle membrane / phagocytic vesicle membrane / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / lamellipodium / Clathrin-mediated endocytosis / late endosome membrane / cytoplasmic vesicle / neuron projection / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / DNA binding / RNA binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å | ||||||
Authors | Evans, P.R. / Owen, D.J. / Luzio, J.P. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: Molecular Basis for the Sorting of the Snare Vamp7 Into Endocytic Clathrin-Coated Vesicles by the Arfgap Hrb. Authors: Pryor, P.R. / Jackson, L. / Gray, S.R. / Edeling, M.A. / Thompson, A. / Sanderson, C.M. / Evans, P.R. / Owen, D.J. / Luzio, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vx8.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vx8.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vx8 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vx8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18681.023 Da / Num. of mol.: 4 Fragment: HRB, RESIDUES 136-175, VAMP7 LONGIN DOMAIN, RESIDUES 1-120 Source method: isolated from a genetically manipulated source Details: CHIMERA OF HUMAN HRB AND MOUSE VAMP7 Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) MUS MUSCULUS (house mouse) Plasmid: PGEX 4T-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52594, UniProt: P70280 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | RESIDUES 44-163 CORRESPOND TO THE LONGIN DOMAIN OF VAMP7 RESIDUES 1-42 ARE FROM HUMAN HRB ...RESIDUES 44-163 CORRESPOND | |
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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: 2.2 Å3/Da / Density % sol: 54.6 % / Description: A SINGLE HG DERIVATIVE WAS USED |
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Crystal grow | pH: 4 Details: 20% PEG 6000, 100MM NA CITRATE PH 4.0, 0.2M LICL, FLASH COOLED IN 22%PEG, 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→78 Å / Num. obs: 34876 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 2.2→57.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.678 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALLISED CHAIN IS A FUSION PROTEIN CORRESPONDING TO RESIDUES 136-176 OF HRB LINKED BY A SINGLE GLYCINE (RESIDUE 43) TO RESIDUES 1- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALLISED CHAIN IS A FUSION PROTEIN CORRESPONDING TO RESIDUES 136-176 OF HRB LINKED BY A SINGLE GLYCINE (RESIDUE 43) TO RESIDUES 1-120 OF VAMP7 THE ASYMMETRIC UNIT CONTAINS 4 MOLECULES. CHAINS C AND D ARE SELF-CONTAINED. CHAINS A & B SWAP THE FIRST 40 RESIDUES OR SO, CORRESPONDING TO THE HRB FRAGMENT
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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: 42.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→57.71 Å
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