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- PDB-3f00: Crystal Structure of Synaptotagmin I C2A domain with Cu(II) -

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Basic information

Entry
Database: PDB / ID: 3f00
TitleCrystal Structure of Synaptotagmin I C2A domain with Cu(II)
ComponentsSynaptotagmin-1
KeywordsMETAL BINDING PROTEIN / Synaptotagmin I / C2A / copper
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 / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / 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 / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin 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
COPPER (II) ION / Synaptotagmin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsGuo, F. / Dakshinamurthy, R. / Thallapuranam, S.K.K. / Sakon, J.
CitationJournal: To be Published
Title: Crystal structure of Synaptotagmin I C2A
Authors: Guo, F. / Dakshinamurthy, R. / Thallapuranam, S.K.K. / Sakon, J.
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2017Group: Structure summary / Category: entity_name_com / Item: _entity_name_com.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)16,2735
Polymers15,9541
Non-polymers3194
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.647, 38.363, 44.016
Angle α, β, γ (deg.)90.000, 98.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15954.164 Da / Num. of mol.: 1 / Fragment: UNP residues 141-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Production host: Escherichia coli (E. coli) / References: UniProt: P21579
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98268 Å
DetectorDetector: CCD / Date: Dec 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98268 Å / Relative weight: 1
ReflectionResolution: 1.36→100 Å / Num. obs: 28585 / % possible obs: 95.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.165 / Χ2: 1.302 / Net I/σ(I): 15.786
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.36-1.412.20.51421770.65973.2
1.41-1.472.70.47427590.59193.2
1.47-1.533.10.40329140.61497.7
1.53-1.613.20.36828900.84397.3
1.61-1.713.40.27128890.71797.3
1.71-1.853.70.27429281.17598.7
1.85-2.034.30.24429811.37999.7
2.03-2.335.10.24929921.55799.9
2.33-2.936.10.2429962.04699.6
2.93-10060.10530591.4399.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RSY

1rsy


Resolution: 1.36→20.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.804 / SU B: 3.108 / SU ML: 0.056 / SU R Cruickshank DPI: 0.087 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1414 5 %RANDOM
Rwork0.201 ---
obs0.203 28466 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 134.3 Å2 / Biso mean: 17.97 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.36→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 12 244 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221199
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9821614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8755140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04325.43957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.12315221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.777153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02883
X-RAY DIFFRACTIONr_nbd_refined0.2840.2568
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2826
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2186
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.237
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.120.21
X-RAY DIFFRACTIONr_mcbond_it1.3972733
X-RAY DIFFRACTIONr_mcangle_it2.09931153
X-RAY DIFFRACTIONr_scbond_it1.2942520
X-RAY DIFFRACTIONr_scangle_it1.8513461
X-RAY DIFFRACTIONr_rigid_bond_restr1.15931215
X-RAY DIFFRACTIONr_sphericity_free3.1423246
X-RAY DIFFRACTIONr_sphericity_bonded3.78231141
LS refinement shellResolution: 1.36→1.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 64 -
Rwork0.341 1266 -
all-1330 -
obs--99.85 %

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