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- PDB-3hd7: HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE... -

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Basic information

Entry
Database: PDB / ID: 3hd7
TitleHELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, spacegroup C 1 2 1
Components
  • (Synaptosomal-associated protein ...) x 2
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsEXOCYTOSIS / MEMBRANE PROTEIN / COILED-COIL / 4-HELICAL BUNDLE / Cell junction / Cytoplasmic vesicle / Membrane / Phosphoprotein / Synapse / Synaptosome / Transmembrane / Neurotransmitter transport / Transport / Cell membrane / Lipoprotein / Palmitate
Function / homology
Function and homology information


trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / zymogen granule membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / vesicle fusion / vesicle docking / positive regulation of calcium ion-dependent exocytosis / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / myosin binding / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / long-term memory / axonal growth cone / response to glucose / presynaptic active zone membrane / vesicle-mediated transport / voltage-gated potassium channel complex / somatodendritic compartment / photoreceptor inner segment / axonogenesis / SNARE binding / acrosomal vesicle / secretory granule / filopodium / locomotory behavior / establishment of localization in cell / long-term synaptic potentiation / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / 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
glycylglycylglycine / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 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
DepositionMay 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,12419
Polymers79,7888
Non-polymers1,33611
Water00
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4648
Polymers39,8944
Non-polymers5704
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-155 kcal/mol
Surface area19590 Å2
MethodPISA
2
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,65911
Polymers39,8944
Non-polymers7667
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-192 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.412, 135.490, 58.689
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number5
Space group name H-MC121
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 188:286 )
112CHAIN A AND (RESSEQ 26:116 )
212CHAIN E AND (RESSEQ 26:115 )
113CHAIN C AND (RESSEQ 9:82 )
213CHAIN G AND (RESSEQ 9:82 )
114CHAIN D AND (RESSEQ 139:200 )
214CHAIN H AND (RESSEQ 139:200 )

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules AEBF

#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

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Synaptosomal-associated protein ... , 2 types, 4 molecules CGDH

#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: Snap25 / 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: Snap25 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P60881

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Non-polymers , 2 types, 11 molecules

#5: Chemical ChemComp-GGG / glycylglycylglycine


Mass: 189.169 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H11N3O4 / Details: Synthetic peptide
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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Details

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: 6.572 Å3/Da / Density % sol: 81.285 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 29% PEG 400, 0.1M HEPES, 0.2M lithium sulfate, 0.1M sodium chloride, 0.03M glycylglycylglycine, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 28140 / % possible obs: 99.8 % / Observed criterion σ(I): 1.8 / Redundancy: 6.9 % / Biso Wilson estimate: 108.7 Å2 / Rsym value: 0.072 / Net I/σ(I): 15.1
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2332 / Rsym value: 0.574 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1N7S

1n7s


Resolution: 3.4→44.203 Å / SU ML: 0.86 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1414 5.06 %RANDOM
Rwork0.239 ---
obs0.2406 27960 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 135.087 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 174.2 Å2
Baniso -1Baniso -2Baniso -3
1--21.848 Å20 Å2-47.578 Å2
2--34.942 Å20 Å2
3----19.913 Å2
Refinement stepCycle: LAST / Resolution: 3.4→44.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 79 0 5322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035341
X-RAY DIFFRACTIONf_angle_d0.6267136
X-RAY DIFFRACTIONf_chiral_restr0.042807
X-RAY DIFFRACTIONf_plane_restr0.001927
X-RAY DIFFRACTIONf_dihedral_angle_d13.9112093
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B779X-RAY DIFFRACTIONPOSITIONAL
12F779X-RAY DIFFRACTIONPOSITIONAL0.316
21A726X-RAY DIFFRACTIONPOSITIONAL
22E726X-RAY DIFFRACTIONPOSITIONAL0.313
31C596X-RAY DIFFRACTIONPOSITIONAL
32G596X-RAY DIFFRACTIONPOSITIONAL0.281
41D496X-RAY DIFFRACTIONPOSITIONAL
42H496X-RAY DIFFRACTIONPOSITIONAL0.279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.4-3.52150.48491270.41552415254289
3.5215-3.66240.39411450.37082669281499
3.6624-3.8290.35051320.29992637276999
3.829-4.03070.32721320.25852679281199
4.0307-4.28310.26151430.2152672281599
4.2831-4.61350.21291430.20227002843100
4.6135-5.07710.21841410.18322639278099
5.0771-5.81040.27461420.241127162857100
5.8104-7.31510.30561610.24927152876100
7.3151-44.20630.21211480.19842704285298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68811.81461.10961.07722.0907-0.1886-0.2024-0.7730.0953-0.53370.02720.3353-0.7123-0.86070.00021.35270.0101-0.24430.6626-0.21781.0514158.598131.3636100.6572
20.06550.01280.01720.07440.0110.0148-0.30380.67350.3357-0.9996-0.1976-0.204-0.18831.3014-0.00031.47310.4885-0.0670.73910.09631.0822128.7156-3.302652.1817
31.1290.51091.2325-0.4320.3880.6023-0.0627-0.1770.27390.2884-0.28770.30650.5317-0.23110.00061.3507-0.2666-0.10880.9326-0.26160.7561156.662829.4162100.8663
40.372-0.6928-0.2508-0.71740.5070.72470.0707-0.34560.2162-0.23920.3991-0.05240.4022-0.65440.00231.6018-0.54820.19621.3749-0.13030.9303164.227136.3919124.2167
50.1402-1.39730.20121.64090.63930.2057-0.66840.28830.5623-0.2019-0.30330.0747-0.88321.7509-0.00090.9013-0.83530.18591.383-0.02270.7812168.415634.0245118.1163
6-0.6061.51490.3092.0871.5177-0.066-0.07180.6227-0.19410.04270.126-0.2553-0.00360.21730.00011.0826-0.3992-0.27541.148-0.06531.568692.3168-24.871730.8493
70.01770.03840.01560.05710.03020.03680.0305-0.2675-0.29730.86140.39-1.3793-0.7111-0.33350.00021.54330.08640.00791.43790.56481.6722131.24223.016953.8181
8-0.07910.97120.51890.72970.45760.18611.1385-0.8588-0.36270.4661-1.2231-0.12670.2702-0.526-0.04850.6939-0.58930.05860.98370.15381.043591.7355-23.137432.6568
90.21120.65190.64480.011-0.4511-0.3851-0.0784-0.1038-0.4205-0.3725-0.0793-0.3917-0.15320.41280.00011.3655-0.52520.03251.6067-0.1991.465270.8683-36.920527.8029
102.18541.17021.12520.0865-0.4784-1.8126-0.46382.9201-0.441-0.00490.9892-0.31340.05820.44890.02450.8869-0.31810.10341.3878-0.5011.099875.9504-32.644622.8675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 26:106)
2X-RAY DIFFRACTION2chain A and resid 107:116)
3X-RAY DIFFRACTION3chain B and resid 189:286)
4X-RAY DIFFRACTION4chain C and resid 8:82)
5X-RAY DIFFRACTION5chain D and resid 138:200)
6X-RAY DIFFRACTION6chain E and resid 26:106)
7X-RAY DIFFRACTION7chain E and resid 107:116)
8X-RAY DIFFRACTION8chain F and resid 189:286)
9X-RAY DIFFRACTION9chain G and resid 8:82)
10X-RAY DIFFRACTION10chain H and resid 138:200)

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