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- PDB-1kil: Three-dimensional structure of the complexin/SNARE complex -

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Basic information

Entry
Database: PDB / ID: 1kil
TitleThree-dimensional structure of the complexin/SNARE complex
Components
  • Complexin I SNARE-complex binding region
  • SNAP-25 C-terminal SNARE motif
  • SNAP-25 N-terminal SNARE motif
  • Synaptobrevin SNARE motif
  • Syntaxin SNARE motif short
KeywordsMEMBRANE PROTEIN / Helix bound to four helix bundle
Function / homology
Function and homology information


regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling ...regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / Toxicity of botulinum toxin type E (botE) / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Lysosome Vesicle Biogenesis / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Toxicity of botulinum toxin type A (botA) / synaptic vesicle docking / zymogen granule membrane / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle priming / Acetylcholine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / storage vacuole / ribbon synapse / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to gravity / vesicle-mediated transport in synapse / positive regulation of calcium ion-dependent exocytosis / Serotonin Neurotransmitter Release Cycle / vesicle docking / eosinophil degranulation / regulation of exocytosis / secretion by cell / SNAP receptor activity / SNARE complex / Dopamine Neurotransmitter Release Cycle / chloride channel inhibitor activity / Norepinephrine Neurotransmitter Release Cycle / vesicle fusion / regulation of vesicle-mediated transport / calcium-ion regulated exocytosis / Cargo recognition for clathrin-mediated endocytosis / LGI-ADAM interactions / Glutamate Neurotransmitter Release Cycle / Clathrin-mediated endocytosis / actomyosin / positive regulation of intracellular protein transport / hormone secretion / Golgi to plasma membrane protein transport / ATP-dependent protein binding / neuron projection terminus / protein localization to membrane / syntaxin binding / regulation of synaptic vesicle recycling / syntaxin-1 binding / clathrin-coated vesicle / insulin secretion / Other interleukin signaling / Sensory processing of sound by inner hair cells of the cochlea / endosomal transport / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / synaptic vesicle priming / regulation of synapse assembly / myosin binding / regulation of neuron projection development / exocytosis / associative learning / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis / tertiary granule membrane / protein sumoylation / synaptic vesicle endocytosis / postsynaptic cytosol / positive regulation of excitatory postsynaptic potential / voltage-gated potassium channel activity / long-term memory / calcium channel inhibitor activity / axonal growth cone / response to glucose / specific granule membrane / vesicle-mediated transport / presynaptic active zone membrane / voltage-gated potassium channel complex / photoreceptor inner segment / calyx of Held / endomembrane system
Similarity search - Function
Single Helix bin / Synaphin / Synaphin protein / Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin ...Single Helix bin / Synaphin / Synaphin protein / Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Synaptobrevin-like / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / Synaptobrevin / 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-1A / Synaptosomal-associated protein 25 / Complexin-1 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, X. / Tomchick, D. / Kovrigin, E. / Arac, D. / Machius, M. / Sudhof, T.C. / Rizo, J.
CitationJournal: Neuron / Year: 2002
Title: Three-dimensional structure of the complexin/SNARE complex.
Authors: Chen, X. / Tomchick, D.R. / Kovrigin, E. / Arac, D. / Machius, M. / Sudhof, T.C. / Rizo, J.
History
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE RESIDUE 10 CHAIN C, THE WILD-TYPE SEQUENCE STARTS WITH LEU11. SER10 IN THE COORDINATES IS ... SEQUENCE RESIDUE 10 CHAIN C, THE WILD-TYPE SEQUENCE STARTS WITH LEU11. SER10 IN THE COORDINATES IS PART OF THE VECTOR GLY9 WHICH IS DISORDERED. RESIDUE 140 CHAIN D, THE WILD-TYPE SEQUENCE STARTS WITH ALA141. BOTH RESIDUES FROM THE VECTOR GLY139 AND SER140 ARE ORDERED. RESIDUE 204 CHAIN D IS AN ENGINEERED TRP(FLUORESCENCE STUDIES) IT IS NOT PART OF THE NATIVE SEQUENCES, THREFORE NOT A MUTATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptobrevin SNARE motif
B: Syntaxin SNARE motif short
C: SNAP-25 N-terminal SNARE motif
D: SNAP-25 C-terminal SNARE motif
E: Complexin I SNARE-complex binding region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9247
Polymers36,8755
Non-polymers492
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-113 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.489, 60.425, 159.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Synaptobrevin SNARE motif / vesicle associated membrane protein 2B


Mass: 7660.553 Da / Num. of mol.: 1 / Fragment: SNARE motif (29-93)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Synaptobrevin 2 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63045
#2: Protein Syntaxin SNARE motif short / synaptotagmin associated associated 35 kDA protein


Mass: 7192.038 Da / Num. of mol.: 1 / Fragment: SNARE motif (191-253)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syntaxin 1A / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32851
#3: Protein SNAP-25 N-terminal SNARE motif / synaptosomal-associated protein 25kD


Mass: 8642.615 Da / Num. of mol.: 1 / Fragment: SNARE motif (11-82) / Mutation: W added at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP-25 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60880
#4: Protein SNAP-25 C-terminal SNARE motif / synaptosomal-associated protein 25kD


Mass: 7613.459 Da / Num. of mol.: 1 / Fragment: SNARE motif (141-203) / Mutation: W added at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP-25 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60880

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Protein/peptide , 1 types, 1 molecules E

#5: Protein/peptide Complexin I SNARE-complex binding region


Mass: 5766.459 Da / Num. of mol.: 1 / Fragment: Complexin (residues 26-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Complexin 1 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63041

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Non-polymers , 2 types, 115 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27%(v/v) Iso-Propanol, 200mM MgCl2, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.5
2130 mM1dropNaCl
310 mg/mlprotein1drop
435 %(v/v)isopropanol1reservoir
5200 mM1reservoirMgCl2
6100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 20, 2001
RadiationMonochromator: Double-crystal monochrmator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→32.2 Å / Num. all: 18098 / Num. obs: 17624 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.3 / Num. unique all: 728 / Rsym value: 0.265 / % possible all: 82.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 14111 / % possible obs: 99.6 % / Num. measured all: 78881 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFC

1sfc


Resolution: 2.3→32.23 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1536401.45 / Data cutoff high rms absF: 1536401.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1005 6.3 %RANDOM
Rwork0.245 ---
all0.287 15857 --
obs-15857 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1732 Å2 / ksol: 0.32352 e/Å3
Displacement parametersBiso mean: 65.7 Å2
Baniso -1Baniso -2Baniso -3
1-36.42 Å20 Å20 Å2
2---4.39 Å20 Å2
3----32.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 2 113 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.932.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 116 5.7 %
Rwork0.361 1920 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.
X-RAY DIFFRACTION3ION.PARAMION.
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 13041 / σ(F): 0 / % reflection Rfree: 6.3 % / Rfactor obs: 0.237 / Rfactor Rfree: 0.303
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 65.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scangle_it3.932.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.361

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