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- PDB-6u4w: 1.4 A structure of a pathogenic human Syt 1 C2B (D366E) -

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Basic information

Entry
Database: PDB / ID: 6u4w
Title1.4 A structure of a pathogenic human Syt 1 C2B (D366E)
ComponentsSynaptotagmin-1
KeywordsEXOCYTOSIS / C2 domain / C2B / Greek Key / Baker-Gordon syndrome
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Toxicity of botulinum toxin type B (botB) ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / chromaffin granule membrane / dense core granule / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / vesicle docking / exocytic vesicle / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of exocytosis / vesicle organization / vesicle fusion / protein heterooligomerization / positive regulation of dopamine secretion / Glutamate Neurotransmitter Release Cycle / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / syntaxin-1 binding / Neurexins and neuroligins / clathrin binding / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / presynaptic active zone / postsynaptic cytosol / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / presynaptic cytosol / regulation of synaptic transmission, glutamatergic / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / SNARE binding / hippocampal mossy fiber to CA3 synapse / clathrin-coated endocytic vesicle membrane / molecular condensate scaffold activity / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / cell differentiation / calmodulin binding / postsynaptic density / neuron projection / protein heterodimerization activity / axon / lipid binding / calcium ion binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / Resolution: 1.4 Å
AuthorsDominguez, M.J. / Bradberry, M.M. / Chapman, E.R. / 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 26, 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

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2785
Polymers17,8941
Non-polymers3844
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.390, 54.390, 103.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 17893.846 Da / Num. of mol.: 1 / Mutation: D366E
Source method: isolated from a genetically manipulated source
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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.6 M Ammonium Sulfate, 0.1 M Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.4→27.91 Å / Num. obs: 35752 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 12.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.082 / Net I/σ(I): 16.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1747 / CC1/2: 0.698 / Rrim(I) all: 1.499 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB-REDOrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOW

1uow


Resolution: 1.4→27.91 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7741
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 1854 5.22 %
Rwork0.1866 33648 -
obs0.188 35502 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.98 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 20 110 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051333
X-RAY DIFFRACTIONf_angle_d1.11631810
X-RAY DIFFRACTIONf_chiral_restr0.0912196
X-RAY DIFFRACTIONf_plane_restr0.0093230
X-RAY DIFFRACTIONf_dihedral_angle_d19.9278519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.78591250.56822469X-RAY DIFFRACTION96.18
1.44-1.480.40931270.33672547X-RAY DIFFRACTION98.16
1.48-1.530.30841450.23622503X-RAY DIFFRACTION98.62
1.53-1.580.21871380.21532562X-RAY DIFFRACTION99.01
1.58-1.650.2341110.19192597X-RAY DIFFRACTION99.34
1.65-1.720.18471420.17622563X-RAY DIFFRACTION99.27
1.72-1.810.20551630.15872594X-RAY DIFFRACTION99.93
1.81-1.930.21581120.1412593X-RAY DIFFRACTION99.89
1.93-2.070.19721400.1422598X-RAY DIFFRACTION99.96
2.07-2.280.18591850.15092583X-RAY DIFFRACTION99.89
2.28-2.610.18581630.16142614X-RAY DIFFRACTION99.57
2.61-3.290.21351410.19712648X-RAY DIFFRACTION99.89
3.29-27.910.18681620.18242777X-RAY DIFFRACTION99.32

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