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- PDB-2nps: Crystal Structure of the Early Endosomal SNARE Complex -

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Basic information

Entry
Database: PDB / ID: 2nps
TitleCrystal Structure of the Early Endosomal SNARE Complex
Components
  • Syntaxin 13
  • Syntaxin-6
  • Vesicle transport through interaction with t-SNAREs homolog 1A
  • Vesicle-associated membrane protein 4
KeywordsTRANSPORT 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 / Retrograde transport at the Trans-Golgi-Network ...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 / : / Golgi ribbon formation / Intra-Golgi traffic / Golgi vesicle transport / Golgi to vacuole transport / vesicle fusion / vesicle docking / clathrin-coated vesicle membrane / voluntary musculoskeletal movement / SNARE complex / Golgi to plasma membrane protein transport / Cargo recognition for clathrin-mediated endocytosis / SNAP receptor activity / intra-Golgi vesicle-mediated transport / protein targeting to vacuole / Clathrin-mediated endocytosis / endocytic recycling / neuron projection terminus / phagophore assembly site / retrograde transport, endosome to Golgi / SNARE complex assembly / syntaxin binding / cholesterol efflux / clathrin-coated vesicle / regulation of synaptic vesicle endocytosis / 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 / synaptic vesicle membrane / microtubule cytoskeleton organization / recycling endosome / autophagy / cellular response to type II interferon / recycling endosome membrane / regulation of protein localization / synaptic vesicle / late endosome membrane / early endosome membrane / vesicle / membrane => GO:0016020 / protein stabilization / early endosome / endosome / membrane raft / Golgi membrane / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Vesicle-associated membrane protein 4 / Syntaxin 6, N-terminal / Syntaxin 6, N-terminal / Syntaxin-like protein / GOSR2/Membrin/Bos1 / Snare region anchored in the vesicle membrane C-terminus / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 ...Vesicle-associated membrane protein 4 / Syntaxin 6, N-terminal / Syntaxin 6, N-terminal / Syntaxin-like protein / GOSR2/Membrin/Bos1 / Snare region anchored in the vesicle membrane C-terminus / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Syntaxin-12 / Syntaxin-6 / Syntaxin-12 / Vesicle-associated membrane protein 4 / Vesicle transport through interaction with t-SNAREs homolog 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZwilling, D. / Cypionka, A. / Pohl, W.H. / Fasshauer, D. / Walla, P.J. / Wahl, M.C. / Jahn, R.
CitationJournal: 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
DepositionOct 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 4
B: Syntaxin 13
C: Vesicle transport through interaction with t-SNAREs homolog 1A
D: Syntaxin-6


Theoretical massNumber of molelcules
Total (without water)35,5074
Polymers35,5074
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-99 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.882, 28.657, 41.887
Angle α, β, γ (deg.)90.00, 98.25, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetrameric coiled-coil comprised of chains A, B, C, and D. There is one biological assembly per asymmetric unit.

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Components

#1: Protein Vesicle-associated membrane protein 4 / VAMP-4


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
#2: Protein Syntaxin 13 /


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 Vesicle transport through interaction with t-SNAREs homolog 1A / Vesicle transport v-SNARE protein Vti1-like 2 / Vti1-rp2


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 Syntaxin-6 /


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1SFC

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
RfactorNum. reflection% reflectionSelection details
Rfree0.289 482 -Random
Rwork0.247 ---
all0.251 10740 --
obs0.251 9365 87.2 %-
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 0 121 2328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00811
X-RAY DIFFRACTIONc_angle_deg1.27675
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0.299
RfactorNum. reflection% reflection
Rfree0.278 10 -
Rwork0.259 --
obs-321 42.5 %

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