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- PDB-3rk3: Truncated SNARE complex with complexin -

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Basic information

Entry
Database: PDB / ID: 3rk3
TitleTruncated SNARE complex with complexin
Components
  • (SNAP25) x 2
  • Complexin-1
  • Syntaxin 1a
  • Vamp2
KeywordsMEMBRANE PROTEIN/EXOCYTOSIS / SNARE proteins / membrane fusion / MEMBRANE PROTEIN-EXOCYTOSIS-TRANSPORT PROTEIN complex / MEMBRANE PROTEIN-EXOCYTOSIS complex
Function / homology
Function and homology information


synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex / 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) / Toxicity of tetanus toxin (tetX) / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) ...synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex / 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) / Toxicity of tetanus toxin (tetX) / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) / myosin head/neck binding / Toxicity of botulinum toxin type D (botD) / trans-Golgi Network Vesicle Budding / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type A (botA) / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Toxicity of botulinum toxin type B (botB) / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / 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 / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / eosinophil degranulation / vesicle fusion / vesicle docking / neurotransmitter transmembrane transporter activity / positive regulation of calcium ion-dependent exocytosis / regulation of neurotransmitter secretion / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / regulation of vesicle-mediated transport / 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 / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / Sensory processing of sound by inner hair cells of the cochlea / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Lysosome Vesicle Biogenesis / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Other interleukin signaling / Golgi Associated Vesicle Biogenesis / myosin binding / Insulin processing / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / calyx of Held / regulation of insulin secretion / positive regulation of excitatory postsynaptic potential / tertiary granule membrane / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity
Similarity search - Function
Single Helix bin / Synaphin / Synaphin protein / 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 ...Single Helix bin / Synaphin / Synaphin protein / 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
Complexin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKuemmel, D. / Reinisch, K.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Complexin cross-links prefusion SNAREs into a zigzag array.
Authors: Kummel, D. / Krishnakumar, S.S. / Radoff, D.T. / Li, F. / Giraudo, C.G. / Pincet, F. / Rothman, J.E. / Reinisch, K.M.
History
DepositionApr 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Sep 13, 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: Vamp2
B: Syntaxin 1a
C: SNAP25
D: SNAP25
E: Complexin-1


Theoretical massNumber of molelcules
Total (without water)35,9695
Polymers35,9695
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-94 kcal/mol
Surface area17010 Å2
Unit cell
Length a, b, c (Å)75.861, 52.729, 128.712
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Vamp2


Mass: 4254.826 Da / Num. of mol.: 1 / Fragment: UNP residues 28-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAMP2, SYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63027
#2: Protein Syntaxin 1a


Mass: 7551.502 Da / Num. of mol.: 1 / Fragment: UNP residues 191-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#3: Protein SNAP25


Mass: 9500.615 Da / Num. of mol.: 1 / Fragment: UNP residues 7-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP25, SNAP / Production host: Escherichia coli (E. coli) / References: UniProt: P60880
#4: Protein SNAP25


Mass: 7427.250 Da / Num. of mol.: 1 / Fragment: UNP residues 141-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP25, SNAP / Production host: Escherichia coli (E. coli) / References: UniProt: P60880
#5: Protein Complexin-1 / Complexin I / CPX I / Synaphin-2


Mass: 7235.150 Da / Num. of mol.: 1 / Fragment: UNP residues 26-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPLX1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14810

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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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2009
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 6465 / % possible obs: 94.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 3.5→3.63 Å / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RK2

3rk2


Resolution: 3.5→32.05 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.875 / SU B: 65.568 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.674 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31631 314 4.8 %RANDOM
Rwork0.26973 ---
obs0.27176 6172 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 99.795 Å2
Baniso -1Baniso -2Baniso -3
1-13.58 Å20 Å210.83 Å2
2---0.24 Å20 Å2
3----11.37 Å2
Refinement stepCycle: LAST / Resolution: 3.5→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 0 0 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0540.032475
X-RAY DIFFRACTIONr_bond_other_d0.0010.021540
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9682942
X-RAY DIFFRACTIONr_angle_other_deg0.77333743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76225.426129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63615453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6331524
X-RAY DIFFRACTIONr_chiral_restr0.0380.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022478
X-RAY DIFFRACTIONr_gen_planes_other00.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.74121634
X-RAY DIFFRACTIONr_mcbond_other0.8592559
X-RAY DIFFRACTIONr_mcangle_it7.09632172
X-RAY DIFFRACTIONr_scbond_it10.9214.5840
X-RAY DIFFRACTIONr_scangle_it17.2496770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 22 -
Rwork0.28 433 -
obs--98.91 %
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)
10.9981-0.7378-3.17676.2706-1.257612.222-0.0906-0.13540.0820.4004-0.0483-0.0491-0.09850.47470.1390.04130.0089-0.06830.1854-0.04010.16442.7544-6.195664.9213
23.08470.113-2.7022.3226-0.21216.777-0.03760.36110.2992-0.17230.11840.0287-0.2693-0.4616-0.08090.05130.0121-0.06110.17270.01370.09483.6148-4.174638.677
30.2519-0.57320.80891.7528-0.92911.2087-0.04590.12880.0124-0.2932-0.4236-0.4947-0.0610.22650.46950.1745-0.02990.09120.23340.02520.344615.8955-6.67328.3271
40.56890.4535-0.59853.1388-3.92246.2144-0.09570.0173-0.1749-0.1819-0.2818-0.46510.02650.54390.37750.0612-0.04310.07440.1476-0.04380.135616.9926-2.932636.0808
50.07480.3577-0.96361.06-3.09979.1895-0.137-0.0491-0.0117-0.0847-0.1994-0.1159-0.02470.34610.33640.2764-0.0154-0.03050.21620.02970.049110.51495.10323.673
62.6261-2.4799-5.00693.07546.334412.2471-0.3595-0.2116-0.4472-0.3162-0.20360.2859-0.5150.2350.56320.54380.0680.10180.40660.030.074310.3183-19.934312.273
70.7811-0.0682-2.14210.14460.26765.2825-0.03610.0313-0.05170.10990.0084-0.14920.0865-0.09120.02770.07860.0258-0.07510.16030.01710.1605-1.7517-17.755267.6458
82.06621.4731-2.75670.931-2.49999.77580.0370.08020.063-0.0840.08030.09120.8875-0.3387-0.11720.1322-0.0354-0.02790.0811-0.00050.23180.7672-28.653773.9012
91.46030.40231.0482-0.35260.59270.573-0.039-0.0599-0.06160.01720.0739-0.0879-0.08290.0499-0.0350.05750.0049-0.08420.1526-0.04980.201711.4384-13.750567.2066
1033.4778-39.021217.469108.1712-45.745826.3304-0.508-4.43421.31990.22442.47772.02560.0843-2.1924-1.96970.0506-0.015-0.02260.6992-0.23830.3839-3.8063-9.675741.6218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 42
2X-RAY DIFFRACTION2A43 - 60
3X-RAY DIFFRACTION3B210 - 250
4X-RAY DIFFRACTION4C30 - 74
5X-RAY DIFFRACTION5D161 - 203
6X-RAY DIFFRACTION6E24 - 69
7X-RAY DIFFRACTION7B189 - 209
8X-RAY DIFFRACTION8C10 - 29
9X-RAY DIFFRACTION9D139 - 160
10X-RAY DIFFRACTION10E70 - 73

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