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- PDB-4wee: High-resolution structure of Synaptotagmin 1 C2A -

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Basic information

Entry
Database: PDB / ID: 4wee
TitleHigh-resolution structure of Synaptotagmin 1 C2A
ComponentsSynaptotagmin-1
KeywordsMETAL BINDING PROTEIN / synaptotagmin / C2 domain / Ca2+ / beta-sandwich
Function / homology
Function and homology information


regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane ...regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / exocytic vesicle / positive regulation of calcium ion-dependent exocytosis / vesicle organization / protein heterooligomerization / positive regulation of dendrite extension / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of dopamine secretion / calcium-ion regulated exocytosis / vesicle fusion / dense core granule / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / neurotransmitter secretion / syntaxin binding / presynaptic active zone / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / excitatory synapse / synaptic vesicle exocytosis / 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 / secretory granule / hippocampal mossy fiber to CA3 synapse / SNARE binding / molecular condensate scaffold activity / response to calcium ion / phospholipid binding / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / presynaptic membrane / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / calcium ion binding / lipid 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.891 Å
AuthorsSutton, R.B. / Fuson, K.L.
Citation
Journal: 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.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold.
Authors: Sutton, R.B. / Davletov, B.A. / Berghuis, A.M. / Sudhof, T.C. / Sprang, S.R.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references / Other
Revision 1.2Sep 27, 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 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Jan 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

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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)16,45010
Polymers16,0971
Non-polymers3539
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.738, 38.547, 44.295
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16097.305 Da / Num. of mol.: 1 / Fragment: UNP residues 140-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.5M ammonium sulfate, 1% PEG400

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.81798 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: 0.81798 Å / Relative weight: 1
ReflectionResolution: 0.7→50 Å / Num. obs: 97100 / % possible obs: 99.5 % / Redundancy: 7 % / Rsym value: 0.033 / Net I/av σ(I): 50 / Net I/σ(I): 50
Reflection shellResolution: 0.89→1.03 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1rsy

1rsy


Resolution: 0.891→19.781 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.164 9710 10 %random selection
Rwork0.1486 ---
obs0.1502 97091 91.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.891→19.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 17 243 1342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121347
X-RAY DIFFRACTIONf_angle_d1.551858
X-RAY DIFFRACTIONf_dihedral_angle_d13.59536
X-RAY DIFFRACTIONf_chiral_restr0.097196
X-RAY DIFFRACTIONf_plane_restr0.009248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8907-0.90080.29491720.30211459X-RAY DIFFRACTION46
0.9008-0.91140.31462150.27871782X-RAY DIFFRACTION57
0.9114-0.92250.27892310.26482031X-RAY DIFFRACTION64
0.9225-0.93420.25072640.24012264X-RAY DIFFRACTION72
0.9342-0.94650.22292460.22822532X-RAY DIFFRACTION78
0.9465-0.95940.24953080.21622591X-RAY DIFFRACTION83
0.9594-0.97310.25263040.2082870X-RAY DIFFRACTION90
0.9731-0.98770.20533400.19242945X-RAY DIFFRACTION93
0.9877-1.00310.19643310.1793034X-RAY DIFFRACTION96
1.0031-1.01950.16483400.16653138X-RAY DIFFRACTION97
1.0195-1.03710.17023260.15423076X-RAY DIFFRACTION98
1.0371-1.0560.16163370.14853165X-RAY DIFFRACTION98
1.056-1.07630.14443360.13883103X-RAY DIFFRACTION98
1.0763-1.09820.1313570.12653147X-RAY DIFFRACTION98
1.0982-1.12210.12933180.12283163X-RAY DIFFRACTION99
1.1221-1.14820.13053520.11913125X-RAY DIFFRACTION98
1.1482-1.17690.12213620.12153143X-RAY DIFFRACTION99
1.1769-1.20880.12663740.11933125X-RAY DIFFRACTION99
1.2088-1.24430.13473820.12453119X-RAY DIFFRACTION99
1.2443-1.28450.14663620.12513161X-RAY DIFFRACTION99
1.2845-1.33040.15393260.13383208X-RAY DIFFRACTION100
1.3304-1.38360.1583460.1323215X-RAY DIFFRACTION100
1.3836-1.44660.15013520.12693166X-RAY DIFFRACTION100
1.4466-1.52280.15123600.13243178X-RAY DIFFRACTION100
1.5228-1.61820.14643590.13623231X-RAY DIFFRACTION100
1.6182-1.74310.15243320.1383215X-RAY DIFFRACTION100
1.7431-1.91830.15373560.14183203X-RAY DIFFRACTION100
1.9183-2.19560.14783940.13753197X-RAY DIFFRACTION100
2.1956-2.7650.1553620.15283215X-RAY DIFFRACTION99
2.765-19.78540.2252660.18292580X-RAY DIFFRACTION77

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