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- PDB-4wy4: Crystal structure of autophagic SNARE complex -

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Basic information

Entry
Database: PDB / ID: 4wy4
TitleCrystal structure of autophagic SNARE complex
Components
  • (Synaptosomal-associated protein 29) x 2
  • Syntaxin-17
  • Vesicle-associated membrane protein 8
KeywordsMEMBRANE PROTEIN / autophagy / SNARE / fusion
Function / homology
Function and homology information


endoplasmic reticulum-Golgi intermediate compartment organization / mucin granule / negative regulation of secretion by cell / ciliary pocket membrane / positive regulation of histamine secretion by mast cell / smooth endoplasmic reticulum membrane / vesicle targeting / trans-Golgi Network Vesicle Budding / synaptic vesicle fusion to presynaptic active zone membrane / zymogen granule membrane ...endoplasmic reticulum-Golgi intermediate compartment organization / mucin granule / negative regulation of secretion by cell / ciliary pocket membrane / positive regulation of histamine secretion by mast cell / smooth endoplasmic reticulum membrane / vesicle targeting / trans-Golgi Network Vesicle Budding / synaptic vesicle fusion to presynaptic active zone membrane / zymogen granule membrane / mitochondria-associated endoplasmic reticulum membrane contact site / Intra-Golgi traffic / mucus secretion / vesicle fusion / vesicle docking / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / protein localization to phagophore assembly site / COPII-mediated vesicle transport / syntaxin binding / SNARE complex assembly / azurophil granule membrane / Lysosome Vesicle Biogenesis / synaptic vesicle priming / Golgi Associated Vesicle Biogenesis / autophagosome membrane docking / COPII-coated ER to Golgi transport vesicle / Golgi organization / exocytosis / endoplasmic reticulum-Golgi intermediate compartment / tertiary granule membrane / autophagosome membrane / autophagosome maturation / cilium assembly / regulation of protein localization to plasma membrane / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / specific granule membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / autophagosome / SNARE binding / secretory granule membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / late endosome membrane / Clathrin-mediated endocytosis / presynapse / ER-Phagosome pathway / early endosome membrane / defense response to virus / protein phosphatase binding / vesicle / membrane fusion / early endosome / symbiont entry into host cell / lysosomal membrane / Golgi membrane / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntaxin-17 / Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Syntaxin / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain ...Syntaxin-17 / Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Syntaxin / 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
Synaptosomal-associated protein 29 / Syntaxin-17 / Vesicle-associated membrane protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsZhao, M. / Brunger, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R37MH63105 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2015
Title: ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes.
Authors: Diao, J. / Liu, R. / Rong, Y. / Zhao, M. / Zhang, J. / Lai, Y. / Zhou, Q. / Wilz, L.M. / Li, J. / Vivona, S. / Pfuetzner, R.A. / Brunger, A.T. / Zhong, Q.
History
DepositionNov 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 8
B: Syntaxin-17
C: Synaptosomal-associated protein 29
D: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)30,4814
Polymers30,4814
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-103 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.850, 35.030, 104.200
Angle α, β, γ (deg.)90.000, 94.090, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Vesicle-associated membrane protein 8 / VAMP-8 / Endobrevin / EDB


Mass: 7623.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAMP8 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BV40
#2: Protein Syntaxin-17


Mass: 6367.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STX17 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56962
#3: Protein Synaptosomal-associated protein 29 / SNAP-29 / Soluble 29 kDa NSF attachment protein / Vesicle-membrane fusion protein SNAP-29


Mass: 8928.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP29 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95721
#4: Protein Synaptosomal-associated protein 29 / SNAP-29 / Soluble 29 kDa NSF attachment protein / Vesicle-membrane fusion protein SNAP-29


Mass: 7561.632 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP29 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95721
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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 Matthews: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M BICINE pH 8.5, 55% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→51.97 Å / Num. obs: 58501 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Χ2: 1.026 / Net I/σ(I): 14.32 / Num. measured all: 385970
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.4-1.440.890.6712.5128653431242310.72698.1
1.44-1.480.9850.3733.9628265425641820.40398.3
1.48-1.520.9930.2225.7527029415040630.24197.9
1.52-1.570.9830.2456.1824913398639150.26798.2
1.57-1.620.9840.2077.324504391238460.22598.3
1.62-1.670.990.179.1725922377937340.18498.8
1.67-1.740.9920.14510.4624649361035820.15799.2
1.74-1.810.9930.12512.0923658350334710.13599.1
1.81-1.890.9940.10513.8622101334233000.11498.7
1.89-1.980.9950.08915.7919421322231730.09798.5
1.98-2.090.9970.07319.8920604306630510.07999.5
2.09-2.210.9960.06723.0819700289728870.07399.7
2.21-2.370.9960.06424.4518181276227450.0799.4
2.37-2.560.9960.06325.3616096250724820.06899
2.56-2.80.9970.05924.8213691236323120.06597.8
2.8-3.130.9970.05826.9413504212020980.06299
3.13-3.610.9960.05428.3612310188618700.05999.2
3.61-4.430.9970.05328.8810632163116220.05899.4
4.43-6.260.9960.04827.337234124712040.05396.6
6.260.9970.05228.9149037397330.05699.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 1.4→51.967 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1768 2919 5 %Random selection based on resolution shells
Rwork0.1363 55467 --
obs0.1383 58386 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.53 Å2 / Biso mean: 28.9173 Å2 / Biso min: 11.88 Å2
Refinement stepCycle: final / Resolution: 1.4→51.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 0 299 2420
Biso mean---45.35 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112371
X-RAY DIFFRACTIONf_angle_d1.1743240
X-RAY DIFFRACTIONf_chiral_restr0.049374
X-RAY DIFFRACTIONf_plane_restr0.006431
X-RAY DIFFRACTIONf_dihedral_angle_d14.225987
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42290.25171360.21762590272698
1.4229-1.44750.27431390.17872642278198
1.4475-1.47380.21661330.1462530266397
1.4738-1.50210.16461360.12832575271196
1.5021-1.53280.15241360.1262593272998
1.5328-1.56610.16721370.11182610274798
1.5661-1.60260.1841400.11382646278698
1.6026-1.64260.15951370.1162604274199
1.6426-1.68710.17421380.12032628276699
1.6871-1.73670.17411400.12152666280699
1.7367-1.79280.18311400.12792652279299
1.7928-1.85680.17371390.1282642278199
1.8568-1.93120.19131390.12722645278499
1.9312-2.01910.1861390.12692630276999
2.0191-2.12550.18251400.125526722812100
2.1255-2.25870.1511420.125726832825100
2.2587-2.43310.16651390.12242645278499
2.4331-2.67790.18281420.13592703284599
2.6779-3.06540.16941390.13912635277498
3.0654-3.86190.17191430.13272715285899
3.8619-52.00310.18361450.16172761290698

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