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- PDB-1uow: Calcium binding domain C2B -

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Basic information

Entry
Database: PDB / ID: 1uow
TitleCalcium binding domain C2B
ComponentsSYNAPTOTAGMIN I
KeywordsGLYCOPROTEIN / LIPOPROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


regulation of vesicle fusion / 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 / calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / Glutamate Neurotransmitter Release Cycle ...regulation of vesicle fusion / 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 / calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / calcium-dependent activation of synaptic vesicle fusion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / dense core granule / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / positive regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / vesicle organization / protein heterooligomerization / vesicle fusion / positive regulation of dopamine secretion / calcium-ion regulated exocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / syntaxin binding / syntaxin-1 binding / clathrin binding / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / 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 / secretory granule / molecular condensate scaffold activity / terminal bouton / phospholipid binding / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / 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 / 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
ACETATE ION / Synaptotagmin-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsCheng, Y. / Sequeira, S.M. / Sollner, T.H. / Patel, D.J.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystallographic Identification of Ca2+ and Sr2+ Coordination Sites in Synaptotagmin I C2B Domain
Authors: Cheng, Y. / Sequeira, S.M. / Malinina, L. / Tereshko, V. / Sollner, T.H. / Patel, D.J.
History
DepositionSep 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNAPTOTAGMIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0545
Polymers17,8231
Non-polymers2314
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.550, 54.550, 103.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SYNAPTOTAGMIN I / SYTI / P65


Mass: 17822.727 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN, RESIDUES 271-421
Source method: isolated from a genetically manipulated source
Details: 2 CALCIUM IONS BOUND, THIS STRUCTURE IS AT THE SAME RESOLUTION AS PDB ENTRY 1TJX, BUT THE LATTER CONTAINS DEPOSITED PROTONS
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOULD PLAY A REGULATORY ROLE IN THE MEMBRANE INTERACTIONS DURING TRAFFICKING OF SYNAPTIC VESICLES ...COULD PLAY A REGULATORY ROLE IN THE MEMBRANE INTERACTIONS DURING TRAFFICKING OF SYNAPTIC VESICLES AT THE ACTIVE ZONE OF SYNAPSES. BINDS ACIDIC PHOSPHOLIPIDS WITH A SPECIFICITY THAT REQUIRES THE PRESENCE OF BOTH AN ACIDIC HEAD GROUP AND A DIACYL BACKBONE.

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorDate: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.04→20 Å / Num. obs: 4126 / % possible obs: 99 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 19.34
Reflection shellResolution: 1.04→1.06 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.62 / % possible all: 96.6

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Processing

Software
NameClassification
REFMACrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5W

1k5w


Resolution: 1.04→20 Å / SU B: 0.332 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026
RfactorNum. reflection% reflectionSelection details
Rfree0.18352 4278 5 %RANDOM
Rwork0.1657 ---
obs0.16658 81211 99.04 %-
Displacement parametersBiso mean: 12.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å20 Å2
2---0.41 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 12 184 1424

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