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- PDB-7u4q: Human Synaptotagmin-1 C2A Y181F Ca2+ bound -

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Basic information

Entry
Database: PDB / ID: 7u4q
TitleHuman Synaptotagmin-1 C2A Y181F Ca2+ bound
ComponentsSynaptotagmin-1
KeywordsEXOCYTOSIS / C2 domain / AD3 / C2A / Greek Key / synaptotagmin
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 / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane ...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 / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / 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 / exocytic vesicle / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle organization / protein heterooligomerization / vesicle docking / positive regulation of dendrite extension / positive regulation of dopamine secretion / regulation of exocytosis / Glutamate Neurotransmitter Release Cycle / vesicle fusion / dense core granule / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / neurotransmitter secretion / presynaptic active zone / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / postsynaptic cytosol / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / clathrin-coated endocytic vesicle membrane / molecular condensate scaffold activity / calcium-dependent protein binding / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / synaptic vesicle membrane / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / lipid binding / calcium ion binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsDominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1R21MH070589-01 United States
CitationJournal: Biophys.J. / Year: 2024
Title: The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability.
Authors: Dominguez, M.J. / Bui, A.A. / Villarreal, J. / Snow, A. / Karmakar, S. / Harsini, F.M. / Rock, P.J. / Rice, A.M. / Fuson, K.L. / Sutton, R.B.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-1
B: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7095
Polymers30,5892
Non-polymers1203
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.810, 99.810, 77.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 15294.448 Da / Num. of mol.: 2 / Fragment: C2A domain / Mutation: Y181F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 100 mM HEPES, 2.3 M malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 81798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 81798 Å / Relative weight: 1
ReflectionResolution: 1.56→26.06 Å / Num. obs: 53881 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 27.28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04023 / Rpim(I) all: 0.01098 / Rrim(I) all: 0.04172 / Net I/σ(I): 27.72
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.899 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 5347 / CC1/2: 0.434 / CC star: 0.778 / Rpim(I) all: 0.6487 / Rrim(I) all: 2.013 / % possible all: 99.63

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
xia2data reduction
xia2data scaling
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wee

4wee


Resolution: 1.56→26.06 Å / SU ML: 0.1841 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.6552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1888 1991 3.7 %
Rwork0.1638 51861 -
obs0.1648 53852 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.59 Å2
Refinement stepCycle: LAST / Resolution: 1.56→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 3 233 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112216
X-RAY DIFFRACTIONf_angle_d1.2533003
X-RAY DIFFRACTIONf_chiral_restr0.0903317
X-RAY DIFFRACTIONf_plane_restr0.0059394
X-RAY DIFFRACTIONf_dihedral_angle_d13.7883831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.33671370.31763664X-RAY DIFFRACTION99.61
1.6-1.640.28171440.26273712X-RAY DIFFRACTION99.77
1.64-1.690.2561420.21453673X-RAY DIFFRACTION100
1.69-1.750.26711380.20223691X-RAY DIFFRACTION99.97
1.75-1.810.24191410.21223673X-RAY DIFFRACTION99.92
1.81-1.880.23641430.19563699X-RAY DIFFRACTION99.95
1.88-1.970.19091410.15243706X-RAY DIFFRACTION99.92
1.97-2.070.19391430.14393664X-RAY DIFFRACTION100
2.07-2.20.18581410.14753707X-RAY DIFFRACTION99.97
2.2-2.370.20521410.14233731X-RAY DIFFRACTION100
2.37-2.610.19711460.14473730X-RAY DIFFRACTION100
2.61-2.980.2121420.18653710X-RAY DIFFRACTION99.97
2.98-3.760.16731440.16413717X-RAY DIFFRACTION100
3.76-26.060.16431480.15173784X-RAY DIFFRACTION99.87

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