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- PDB-1gl2: Crystal structure of an endosomal SNARE core complex -

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Basic information

Entry
Database: PDB / ID: 1gl2
TitleCrystal structure of an endosomal SNARE core complex
Components
  • ENDOBREVIN
  • SYNTAXIN 7
  • SYNTAXIN 8
  • VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1
KeywordsMEMBRANE PROTEIN / MEMBRANE FUSION PROTEIN COMPLEX / COILED COIL / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


zymogen granule exocytosis / positive regulation of pancreatic amylase secretion / mucin granule / negative regulation of secretion by cell / positive regulation of histamine secretion by mast cell / synaptic vesicle to endosome fusion / ER-Phagosome pathway / zymogen granule / trans-Golgi Network Vesicle Budding / basolateral part of cell ...zymogen granule exocytosis / positive regulation of pancreatic amylase secretion / mucin granule / negative regulation of secretion by cell / positive regulation of histamine secretion by mast cell / synaptic vesicle to endosome fusion / ER-Phagosome pathway / zymogen granule / trans-Golgi Network Vesicle Budding / basolateral part of cell / Lysosome Vesicle Biogenesis / zymogen granule membrane / mucus secretion / Golgi Associated Vesicle Biogenesis / Platelet degranulation / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / early endosome to late endosome transport / chloride channel inhibitor activity / Clathrin-mediated endocytosis / basal part of cell / SNARE complex / SNAP receptor activity / vesicle fusion / syntaxin binding / Neutrophil degranulation / azurophil granule membrane / endosome to lysosome transport / SNARE complex assembly / autophagosome membrane docking / regulation of endocytosis / autophagosome maturation / regulation of protein localization to plasma membrane / phagocytic vesicle / vesicle-mediated transport / endomembrane system / secretory granule / secretory granule membrane / SNARE binding / intracellular protein transport / establishment of localization in cell / trans-Golgi network / recycling endosome / cellular response to type II interferon / recycling endosome membrane / synaptic vesicle membrane / late endosome membrane / late endosome / protein transport / protein-containing complex assembly / midbody / early endosome membrane / basolateral plasma membrane / defense response to virus / vesicle / membrane fusion / early endosome / lysosome / endosome / lysosomal membrane / ubiquitin protein ligase binding / symbiont entry into host cell / perinuclear region of cytoplasm / cell surface / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Syntaxin-8, SNARE domain / Syntaxin-like protein / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE protein N-terminus / Vesicle transport v-SNARE, N-terminal domain superfamily / Snare region anchored in the vesicle membrane C-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like ...Syntaxin-8, SNARE domain / Syntaxin-like protein / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE protein N-terminus / Vesicle transport v-SNARE, N-terminal domain superfamily / Snare region anchored in the vesicle membrane C-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / 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-7 / Vesicle transport through interaction with t-SNAREs homolog 1B / Vesicle-associated membrane protein 8 / Syntaxin-8
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAntonin, W. / Becker, S. / Jahn, R. / Schneider, T.R.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure of the Endosomal Snare Complex Reveals Common Structural Principles of All Snares.
Authors: Antonin, W. / Fasshauer, D. / Becker, S. / Jahn, R. / Schneider, T.R.
History
DepositionAug 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 30, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct
Item: _pdbx_struct_assembly.method_details / _struct.title
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOBREVIN
B: SYNTAXIN 7
C: VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1
D: SYNTAXIN 8


Theoretical massNumber of molelcules
Total (without water)29,5844
Polymers29,5844
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-91 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.700, 41.100, 51.500
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOBREVIN


Mass: 7361.149 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 6-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9WUF4
#2: Protein SYNTAXIN 7


Mass: 7325.043 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 169-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O70439
#3: Protein VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1 / VTI1B


Mass: 7551.417 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 140-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O88384
#4: Protein SYNTAXIN 8


Mass: 7346.017 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 149-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Z2Q7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1

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Sample preparation

CrystalDensity % sol: 30 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: PROTEIN SOLUTION: 20 MG/ML OF QUATERNARY COMPLEX IN 20MM TRIS-HCL AT PH 7.4 WELL SOLUTION: 0.1M NA-ACETATE AT PH 5.2, 2.5 M NA-FORMIAT, 15% GLYCEROL HANGING DROPS WITH 2MUL + 2 MUL
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris-HCl1droppH7.4
30.1 Msodium acetate1reservoirpH5.2
42.5 Msodium formate1reservoir
515 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS M18X / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2001 / Details: COSMIC MIRRORS CMF12-38CU6
RadiationMonochromator: COSMIC MIRRORS CMF12-38CU6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 71259 / % possible obs: 93.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.0345 / Net I/σ(I): 30.57
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 11.35 / % possible all: 88.8
Reflection
*PLUS
Num. obs: 14969 / Num. measured all: 71259 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 88.8 % / Redundancy: 3.6 % / Mean I/σ(I) obs: 11.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFC

1sfc


Resolution: 1.9→14.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.224 737 5 %RANDOM
Rwork0.176 ---
obs0.176 14797 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.7879 Å2 / ksol: 0.418194 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.34 Å20 Å21.15 Å2
2---2.53 Å20 Å2
3----4.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 234 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d13.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 118 5.2 %
Rwork0.196 2143 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.58

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