+Open data
-Basic information
Entry | Database: PDB / ID: 2nps | ||||||
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Title | Crystal Structure of the Early Endosomal SNARE Complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Vesicle fusion / SNARE complex / early endosomal SNARE complex / syntaxin 6 / syntaxin 13 / Vti1a / VAMP4 | ||||||
Function / homology | Function and homology information regulation of Golgi to plasma membrane protein transport / : / synaptic vesicle to endosome fusion / Retrograde transport at the Trans-Golgi-Network / : / : / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / postsynaptic recycling endosome / vesicle fusion with Golgi apparatus ...regulation of Golgi to plasma membrane protein transport / : / synaptic vesicle to endosome fusion / Retrograde transport at the Trans-Golgi-Network / : / : / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / postsynaptic recycling endosome / vesicle fusion with Golgi apparatus / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / Golgi vesicle transport / Golgi ribbon formation / Golgi to vacuole transport / vesicle fusion / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / SNARE complex / voluntary musculoskeletal movement / SNAP receptor activity / clathrin-coated vesicle membrane / protein targeting to vacuole / Clathrin-mediated endocytosis / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / endocytic recycling / neuron projection terminus / retrograde transport, endosome to Golgi / phagophore assembly site / syntaxin binding / SNARE complex assembly / regulation of synaptic vesicle endocytosis / clathrin-coated vesicle / cholesterol efflux / autophagosome assembly / autophagosome / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / phagocytic vesicle / SNARE binding / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / ER to Golgi transport vesicle membrane / terminal bouton / recycling endosome / cellular response to type II interferon / synaptic vesicle membrane / microtubule cytoskeleton organization / autophagy / recycling endosome membrane / regulation of protein localization / synaptic vesicle / early endosome membrane / late endosome membrane / vesicle / membrane => GO:0016020 / endosome / early endosome / protein stabilization / membrane raft / Golgi membrane / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zwilling, D. / Cypionka, A. / Pohl, W.H. / Fasshauer, D. / Walla, P.J. / Wahl, M.C. / Jahn, R. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Early endosomal SNAREs form a structurally conserved SNARE complex and fuse liposomes with multiple topologies Authors: Zwilling, D. / Cypionka, A. / Pohl, W.H. / Fasshauer, D. / Walla, P.J. / Wahl, M.C. / Jahn, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nps.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nps.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/2nps ftp://data.pdbj.org/pub/pdb/validation_reports/np/2nps | HTTPS FTP |
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-Related structure data
Related structure data | 1sfcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetrameric coiled-coil comprised of chains A, B, C, and D. There is one biological assembly per asymmetric unit. |
-Components
#1: Protein | Mass: 8687.821 Da / Num. of mol.: 1 / Fragment: VAMP4 SNARE Motif, residues 47-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vamp4_predicted / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O70480 |
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#2: Protein | Mass: 8149.168 Da / Num. of mol.: 1 / Fragment: Syntaxin 13 SNARE Motif, residues 177-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: syntaxin 13 / Plasmid: pEt28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O70319, UniProt: G3V7P1*PLUS |
#3: Protein | Mass: 9548.797 Da / Num. of mol.: 1 / Fragment: Vti1a SNARE Motif, residues 122-199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vti1a / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JI51 |
#4: Protein | Mass: 9121.297 Da / Num. of mol.: 1 Fragment: Syntaxin 6 SNARE Motif, t-SNARE coiled-coil homology, residues 169-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STX6 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43752 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M trisodium citrate dihydrate, 36% (v/v) 2-methyl-2,4-pentandiol, 0.2M Li2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 10740 / Num. obs: 9365 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.039 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / Num. unique all: 827 / Rsym value: 0.309 / % possible all: 46.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1SFC Resolution: 2.5→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 53.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Rfactor Rfree error: 0.299
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