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- PDB-6tz3: Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+ -

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Basic information

Entry
Database: PDB / ID: 6tz3
TitleCrystal Structure of Human Synaptotagmin 1 C2B without Ca2+
ComponentsSynaptotagmin-1
KeywordsEXOCYTOSIS / C2 domain / C2B / Greek Key
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / Acetylcholine Neurotransmitter Release Cycle / regulation of regulated secretory pathway ...clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / Acetylcholine Neurotransmitter Release Cycle / regulation of regulated secretory pathway / calcium ion sensor activity / clathrin-sculpted monoamine transport vesicle membrane / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / regulation of exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / syntaxin binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / chemical synaptic transmission / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 Å
AuthorsDominguez, M.J. / Karmakar, S. / Meyer, A.G. / Sutton, R.B.
CitationJournal: Neuron / Year: 2020
Title: Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.
Authors: Bradberry, M.M. / Courtney, N.A. / Dominguez, M.J. / Lofquist, S.M. / Knox, A.T. / Sutton, R.B. / Chapman, E.R.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1684
Polymers17,8801
Non-polymers2883
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.594, 54.594, 103.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein Synaptotagmin-1 / / Synaptotagmin I / SytI / p65


Mass: 17879.818 Da / Num. of mol.: 1 / Fragment: C2B domain, residues 272-422
Source method: isolated from a genetically manipulated source
Details: orginally cloned from human brain cDNA library / Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SYT1, SVP65, SYT / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.66 % / Mosaicity: 0.337 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M Ammonium Sulfate, 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.097 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 59591 / % possible obs: 97.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Χ2: 0.972 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.17-1.194.60.29930100.9410.1510.3370.95699.4
1.19-1.214.70.24830100.9560.1240.2780.91499.2
1.21-1.244.80.22330010.9650.1110.250.91999.2
1.24-1.264.80.20429590.9680.1010.2280.92398.6
1.26-1.294.70.18129850.9730.090.2030.97998.8
1.29-1.324.80.16329860.9780.0810.1831.00298.5
1.32-1.354.70.14430050.9830.0720.1620.99398.5
1.35-1.394.70.12629410.9870.0630.1410.97698.6
1.39-1.434.80.11330100.9890.0560.1271.03898.7
1.43-1.474.70.09230330.9910.0460.1041.04298.8
1.47-1.534.70.07930120.9930.040.0890.96999
1.53-1.594.70.06930090.9940.0340.0770.99199.4
1.59-1.664.70.06530600.9950.0330.0731.00399.8
1.66-1.754.70.06730440.9940.0340.0751.18799.7
1.75-1.864.60.06630560.9930.0340.0741.42799.6
1.86-24.50.06130670.9940.0320.0691.46899.7
2-2.24.30.04730660.9960.0250.0531.10698.9
2.2-2.524.70.03330470.9980.0170.0370.65398.6
2.52-3.185.20.02630910.9990.0130.030.46397.6
3.18-504.30.02121990.9990.0110.0240.3366.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.53 Å26.4 Å
Translation4.53 Å26.4 Å

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.16_3549refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOW

1uow


Resolution: 1.17→26.4 Å / SU ML: 0.0767 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1992 3.37 %Random selection
Rwork0.1554 57053 --
obs0.1561 59045 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.37 Å2
Refinement stepCycle: LAST / Resolution: 1.17→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 15 179 1377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271269
X-RAY DIFFRACTIONf_angle_d1.24531721
X-RAY DIFFRACTIONf_chiral_restr0.3766196
X-RAY DIFFRACTIONf_plane_restr0.0075214
X-RAY DIFFRACTIONf_dihedral_angle_d13.5498484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.20.17211290.14613703X-RAY DIFFRACTION88.79
1.2-1.230.17571410.13114051X-RAY DIFFRACTION97.38
1.23-1.270.15791440.12414144X-RAY DIFFRACTION98.57
1.27-1.310.14751410.12384093X-RAY DIFFRACTION98.67
1.31-1.360.17191430.12754135X-RAY DIFFRACTION98.55
1.36-1.410.14561470.11934122X-RAY DIFFRACTION98.5
1.41-1.470.16031460.11484169X-RAY DIFFRACTION98.79
1.47-1.550.12781510.11164145X-RAY DIFFRACTION99.24
1.55-1.650.1281440.1144196X-RAY DIFFRACTION99.52
1.65-1.780.18741450.12324201X-RAY DIFFRACTION99.63
1.78-1.960.14251500.1294237X-RAY DIFFRACTION99.75
1.96-2.240.14421450.13694197X-RAY DIFFRACTION98.91
2.24-2.820.18421480.16424274X-RAY DIFFRACTION98.99
2.82-26.40.22411180.21353386X-RAY DIFFRACTION75.35

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