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- PDB-1rsy: STRUCTURE OF THE FIRST C2-DOMAIN OF SYNAPTOTAGMIN I: A NOVEL CA2+... -

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Basic information

Entry
Database: PDB / ID: 1rsy
TitleSTRUCTURE OF THE FIRST C2-DOMAIN OF SYNAPTOTAGMIN I: A NOVEL CA2+(SLASH)PHOSPHOLIPID BINDING FOLD
ComponentsSYNAPTOTAGMIN I
KeywordsCALCIUM/PHOSPHOLIPID BINDING PROTEIN / CALCIUM-PHOSPHOLIPID BINDING PROTEIN complex
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 / calcium-dependent activation of synaptic vesicle fusion / positive regulation of vesicle fusion / chromaffin granule membrane / positive regulation of calcium ion-dependent exocytosis of neurotransmitter ...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 / calcium-dependent activation of synaptic vesicle fusion / positive regulation of vesicle fusion / chromaffin granule membrane / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / calcium ion sensor activity / protein heterooligomerization / exocytic vesicle / positive regulation of calcium ion-dependent exocytosis / vesicle organization / positive regulation of dendrite extension / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / vesicle fusion / positive regulation of dopamine secretion / calcium-dependent phospholipid binding / dense core granule / membraneless organelle assembly / neurotransmitter secretion / presynaptic active zone / syntaxin binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / neuron projection terminus / regulation of dopamine secretion / synaptic vesicle exocytosis / detection of calcium ion / postsynaptic cytosol / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / excitatory synapse / 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 / Resolution: 1.9 Å
AuthorsSutton, R.B. / Sprang, S.R.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: A Single C2 Domain from Synaptotagmin I is Sufficient for High Affinity Ca2+(Slash)Phospholipid Binding
Authors: Davletov, B.A. / Sudhof, T.C.
History
DepositionFeb 1, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: SYNAPTOTAGMIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1942
Polymers17,0981
Non-polymers961
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.300, 38.900, 44.600
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 187

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Components

#1: Protein SYNAPTOTAGMIN I


Mass: 17098.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / References: UniProt: P21707
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHET GROUP TRIVIAL NAME: SULFATE EMPIRICAL FORMULA: SO4 NUMBER OF ATOMS IN GROUP: 5 ADDITIONAL ...HET GROUP TRIVIAL NAME: SULFATE EMPIRICAL FORMULA: SO4 NUMBER OF ATOMS IN GROUP: 5 ADDITIONAL COMMENTS: SULFATE THOUGHT TO MIMIC PHOSPHOLIPID BINDING SITE WATER HOH 154 IS THE SITE OF CALCIUM BINDING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22.0 M1reservoirLi2SO4
3100 mMBES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11214 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 2.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.249 --
Rwork0.186 --
obs0.186 9851 90 %
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 5 80 1151
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.353
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.353

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