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- PDB-1l4a: X-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE ... -

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Basic information

Entry
Database: PDB / ID: 1l4a
TitleX-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE SQUID LOLIGO PEALEI
Components
  • (S-SNAP25 fusion ...) x 2
  • S-SYNTAXIN
  • SYNAPHIN A
  • SYNAPTOBREVIN
KeywordsENDOCYTOSIS/EXOCYTOSIS / SNARE / SNARE complex / membrane fusion / neurotransmission / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


synaptic vesicle fusion to presynaptic active zone membrane / vesicle docking / regulation of neurotransmitter secretion / SNARE complex / SNAP receptor activity / vesicle fusion / syntaxin binding / neurotransmitter transport / synaptic vesicle priming / exocytosis ...synaptic vesicle fusion to presynaptic active zone membrane / vesicle docking / regulation of neurotransmitter secretion / SNARE complex / SNAP receptor activity / vesicle fusion / syntaxin binding / neurotransmitter transport / synaptic vesicle priming / exocytosis / synaptic vesicle exocytosis / vesicle-mediated transport / endomembrane system / SNARE binding / intracellular protein transport / terminal bouton / synaptic vesicle membrane / presynapse / neuron projection / plasma membrane / cytosol
Similarity search - Function
Synaphin / Synaphin protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain ...Synaphin / Synaphin protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Syntaxin / Synaptobrevin / Synaptosomal-associated protein / Complexin
Similarity search - Component
Biological speciesLoligo pealei (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsBracher, A. / Kadlec, J. / Betz, H. / Weissenhorn, W.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: X-ray structure of a neuronal complexin-SNARE complex from squid.
Authors: Bracher, A. / Kadlec, J. / Betz, H. / Weissenhorn, W.
History
DepositionMar 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: SYNAPTOBREVIN
B: S-SYNTAXIN
C: S-SNAP25 fusion protein
D: S-SNAP25 fusion protein
E: SYNAPHIN A


Theoretical massNumber of molelcules
Total (without water)47,5175
Polymers47,5175
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-114 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.072, 75.430, 243.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains the biologically relevant structure

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Components

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Protein , 3 types, 3 molecules ABE

#1: Protein SYNAPTOBREVIN


Mass: 9046.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pRSet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: P47194
#2: Protein S-SYNTAXIN


Mass: 9981.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pMal-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: O46345
#5: Protein SYNAPHIN A


Mass: 9251.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pMal-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: Q95PA1

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S-SNAP25 fusion ... , 2 types, 2 molecules CD

#3: Protein S-SNAP25 fusion protein


Mass: 9566.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pRSet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: Q8T3S4
#4: Protein S-SNAP25 fusion protein


Mass: 9671.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pRSet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: Q8T3S4

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Non-polymers , 1 types, 23 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.55 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 5% MPD, 7.5% PEG550-MME, 20MM beta mercaptoethanol, 20MM Tris PH 7.2, 50MM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
24-5.5 %(v/v)MPD1drop
37-8 %(w/v)PEG550 MME1drop
420 mMbeta-mercaptoethanol1drop
510 %(w/v)MPD1reservoir
616 %(w/v)PEG550 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.95→15 Å / Num. all: 10799 / Num. obs: 10128 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 79.04 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 4.7
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.1 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 75 Å / Num. measured all: 41657 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.219

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Processing

Software
NameVersionClassification
BEASTmodel building
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFC

1sfc


Resolution: 2.95→15 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3445 700 7 %RANDOM
Rwork0.297 ---
all0.3004 10799 --
obs0.3004 10001 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2327 Å2 / ksol: 0.26842 e/Å3
Displacement parametersBiso mean: 81.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.79 Å20 Å20 Å2
2--42.41 Å20 Å2
3----38.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 0 23 2381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 100 6.3 %
Rwork0.346 1484 -
obs-1584 91.8 %
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor all: 0.3004 / Rfactor Rfree: 0.3445 / Rfactor Rwork: 0.297
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.397 / Rfactor Rwork: 0.346

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