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- PDB-3ipd: Helical extension of the neuronal SNARE complex into the membrane... -

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Basic information

Entry
Database: PDB / ID: 3ipd
TitleHelical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21
Components
  • (Synaptosomal-associated protein 25) x 2
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsEXOCYTOSIS / MEMBRANE PROTEIN / COILED COIL / 4-HELICAL BUNDLE / MEMBRANE FUSION / CYTOPLASMIC VESICLE / MEMBRANE / PHOSPHOPROTEIN / SYNAPSE / SYNAPTOSOME / TRANSMEMBRANE / NEUROTRANSMITTER TRANSPORT / TRANSPORT / CELL MEMBRANE / CYTOPLASM / LIPOPROTEIN / PALMITATE / TRANSPORT PROTEIN / Acetylation / Cell junction / Alternative splicing
Function / homology
Function and homology information


exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / BLOC-1 complex / Lysosome Vesicle Biogenesis / myosin head/neck binding / zymogen granule membrane / storage vacuole / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling ...exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / BLOC-1 complex / Lysosome Vesicle Biogenesis / myosin head/neck binding / zymogen granule membrane / storage vacuole / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulated exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle-mediated transport in synapse / positive regulation of intracellular protein transport / regulation of establishment of protein localization / positive regulation of calcium ion-dependent exocytosis / ribbon synapse / regulation of vesicle-mediated transport / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / secretion by cell / chloride channel inhibitor activity / Clathrin-mediated endocytosis / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / positive regulation of hormone secretion / neuron projection terminus / Golgi to plasma membrane protein transport / ATP-dependent protein binding / neurotransmitter secretion / protein localization to membrane / clathrin-coated vesicle / syntaxin binding / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / endosomal transport / Neutrophil degranulation / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / regulation of synapse assembly / myosin binding / synaptic vesicle priming / response to gravity / regulation of neuron projection development / exocytosis / associative learning / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis / protein sumoylation / synaptic vesicle endocytosis / voltage-gated potassium channel activity / positive regulation of excitatory postsynaptic potential / long-term memory / response to glucose / postsynaptic cytosol / axonal growth cone / calcium channel inhibitor activity / vesicle-mediated transport / presynaptic active zone membrane / somatodendritic compartment / voltage-gated potassium channel complex / photoreceptor inner segment / endomembrane system / acrosomal vesicle / axonogenesis / cytoplasmic vesicle membrane / secretory granule / SNARE binding / filopodium / locomotory behavior / intracellular protein transport / establishment of localization in cell / trans-Golgi network
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin / 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
Similarity search - Domain/homology
Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.8 Å
AuthorsStein, A. / Weber, G. / Wahl, M.C. / Jahn, R.
CitationJournal: Nature / Year: 2009
Title: Helical extension of the neuronal SNARE complex into the membrane
Authors: Stein, A. / Weber, G. / Wahl, M.C. / Jahn, R.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionSep 1, 2009ID: 3HD9
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25


Theoretical massNumber of molelcules
Total (without water)79,7888
Polymers79,7888
Non-polymers00
Water00
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25


Theoretical massNumber of molelcules
Total (without water)39,8944
Polymers39,8944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-113 kcal/mol
Surface area19840 Å2
MethodPISA
2
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25


Theoretical massNumber of molelcules
Total (without water)39,8944
Polymers39,8944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-115 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.852, 215.680, 262.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 189:286 )
211CHAIN F AND (RESSEQ 189:286 )
112CHAIN A AND (RESSEQ 26:115 )
212CHAIN E AND (RESSEQ 26:115 )
113CHAIN C AND (RESSEQ 8:82 )
213CHAIN G AND (RESSEQ 8:82 )
114CHAIN D AND (RESSEQ 138:200 )
214CHAIN H AND (RESSEQ 138:200 )

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Vesicle-associated membrane protein 2 / VAMP-2 / Synaptobrevin-2


Mass: 10493.321 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP Residues 30-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P63045
#2: Protein Syntaxin-1A / Synaptotagmin-associated 35 kDa protein / P35A / Neuron-specific antigen HPC-1


Mass: 12334.396 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP Residues 183-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P32851
#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Synaptosomal-associated 25 kDa protein / Super protein / SUP


Mass: 9312.390 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, UNP Residues 7-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SNAP-25 SPLICE VARIANT A / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP-25 / Synaptosomal-associated 25 kDa protein / Super protein / SUP


Mass: 7753.646 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP Residues 141-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SNAP-25 SPLICE VARIANT A / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P60881
Sequence detailsTHE SEQUENCE OF ENTITY 3 AND 4 ARE BASED ON ISOFORM 2 OF UNIPROTKB/SWISS-PROT P60881 (SNP25_RAT).

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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: 9.7551 Å3/Da / Density % sol: 87.3912 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 16% MPD, 0.1M TRIS, 0.05M MAGNESIUM CHLORIDE, 3% SORBITOL, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 4.8→50 Å / Num. all: 16049 / Num. obs: 15646 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 186.97 Å2 / Rsym value: 0.112 / Net I/σ(I): 11.1
Reflection shellResolution: 4.8→4.88 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.51 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HD7

3hd7


Resolution: 4.8→49.884 Å / FOM work R set: 0.655 / SU ML: 3.23
Isotropic thermal model: ISOTROPIC, ONE B-FACTOR PER RESIDUE
σ(F): 0.11 / Phase error: 38.52
RfactorNum. reflection% reflectionSelection details
Rfree0.3318 662 5.02 %RANDOM
Rwork0.3039 ---
obs0.3051 13184 84.16 %-
all-15646 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 195.108 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso max: 503.48 Å2 / Biso mean: 289.334 Å2 / Biso min: 175.12 Å2
Baniso -1Baniso -2Baniso -3
1-172.395 Å20 Å20 Å2
2---52.402 Å2-0 Å2
3----119.993 Å2
Refinement stepCycle: LAST / Resolution: 4.8→49.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 0 0 5242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045272
X-RAY DIFFRACTIONf_angle_d0.6967046
X-RAY DIFFRACTIONf_dihedral_angle_d15.0642082
X-RAY DIFFRACTIONf_chiral_restr0.047808
X-RAY DIFFRACTIONf_plane_restr0.002918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B779X-RAY DIFFRACTIONPOSITIONAL0.019
12F779X-RAY DIFFRACTIONPOSITIONAL0.019
21A726X-RAY DIFFRACTIONPOSITIONAL0.025
22E726X-RAY DIFFRACTIONPOSITIONAL0.025
31C607X-RAY DIFFRACTIONPOSITIONAL0.013
32G607X-RAY DIFFRACTIONPOSITIONAL0.013
41D502X-RAY DIFFRACTIONPOSITIONAL0.014
42H502X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.8-5.17030.43361090.34192171X-RAY DIFFRACTION74
5.1703-5.68990.41021240.35672136X-RAY DIFFRACTION73
5.6899-6.51170.34891200.32052395X-RAY DIFFRACTION81
6.5117-8.19820.28691640.22222741X-RAY DIFFRACTION92
8.1982-49.88640.28841450.29863079X-RAY DIFFRACTION99

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