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- PDB-5vfg: Synaptotagmin 1 C2B domain, lead-bound (high occupancy) -

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Basic information

Entry
Database: PDB / ID: 5vfg
TitleSynaptotagmin 1 C2B domain, lead-bound (high occupancy)
ComponentsSynaptotagmin-1
KeywordsMETAL BINDING PROTEIN / C2B DOMAIN
Function / homology
Function and homology information


GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding ...GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / dense core granule / positive regulation of vesicle fusion / chromaffin granule membrane / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of dopamine secretion / protein heterooligomerization / Clathrin-mediated endocytosis / neurotransmitter secretion / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / regulation of synaptic vesicle exocytosis / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / 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 / secretory granule / phospholipid binding / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / 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
LEAD (II) ION / Synaptotagmin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTaylor, A.B. / Hart, P.J. / Igumenova, T.I.
CitationJournal: Metallomics / Year: 2018
Title: High affinity interactions of Pb2+with synaptotagmin I.
Authors: Katti, S. / Her, B. / Srivastava, A.K. / Taylor, A.B. / Lockless, S.W. / Igumenova, T.I.
History
DepositionApr 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4152
Polymers17,2081
Non-polymers2071
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-0 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.524, 41.277, 83.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17208.006 Da / Num. of mol.: 1 / Fragment: residues 271-421 / Mutation: C277S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt1 / Plasmid: PET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46096
#2: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium fluoride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.82→41.28 Å / Num. obs: 13019 / % possible obs: 99.2 % / Redundancy: 3 % / Biso Wilson estimate: 15.7 Å2 / Rpim(I) all: 0.073 / Rsym value: 0.108 / Net I/σ(I): 7.9
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1856 / Rpim(I) all: 0.365 / Rsym value: 0.532 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOW

1uow


Resolution: 1.82→20.639 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2589 2352 10.03 %
Rwork0.1993 --
obs0.2052 12971 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.82→20.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 1 229 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071244
X-RAY DIFFRACTIONf_angle_d0.8231679
X-RAY DIFFRACTIONf_dihedral_angle_d20.849477
X-RAY DIFFRACTIONf_chiral_restr0.073189
X-RAY DIFFRACTIONf_plane_restr0.005212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8201-1.85720.31661400.29161243X-RAY DIFFRACTION97
1.8572-1.89760.43931330.33241237X-RAY DIFFRACTION97
1.8976-1.94170.39981310.34351255X-RAY DIFFRACTION96
1.9417-1.99020.37281400.25911227X-RAY DIFFRACTION96
1.9902-2.04390.23351450.22891239X-RAY DIFFRACTION97
2.0439-2.1040.28761320.25041233X-RAY DIFFRACTION96
2.104-2.17190.28761300.21641255X-RAY DIFFRACTION97
2.1719-2.24940.34121370.29351250X-RAY DIFFRACTION97
2.2494-2.33940.32711520.2671201X-RAY DIFFRACTION96
2.3394-2.44570.26241450.19071249X-RAY DIFFRACTION98
2.4457-2.57440.23011430.18681269X-RAY DIFFRACTION98
2.5744-2.73530.24861390.17651263X-RAY DIFFRACTION98
2.7353-2.9460.24091350.18951230X-RAY DIFFRACTION97
2.946-3.24140.21421330.17941268X-RAY DIFFRACTION98
3.2414-3.70810.19711320.14711245X-RAY DIFFRACTION96
3.7081-4.66290.24261400.13811236X-RAY DIFFRACTION96
4.6629-20.63980.1891450.14241191X-RAY DIFFRACTION93

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