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- PDB-5vfe: Synaptotagmin 1 C2A domain, lead-bound -

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Basic information

Entry
Database: PDB / ID: 5vfe
TitleSynaptotagmin 1 C2A domain, lead-bound
ComponentsSynaptotagmin-1
KeywordsMETAL BINDING PROTEIN / C2A 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: 1.38 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 ...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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-1
B: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6586
Polymers29,0512
Non-polymers6074
Water6,359353
1
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8293
Polymers14,5261
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8293
Polymers14,5261
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.040, 55.040, 77.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 14525.588 Da / Num. of mol.: 2 / Fragment: residues 140-265
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.: 2 / Source method: obtained synthetically / Formula: Pb
#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.: 353 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% 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: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.38→40.55 Å / Num. obs: 53772 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 13.6 Å2 / Rpim(I) all: 0.022 / Rsym value: 0.064 / Net I/σ(I): 18
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7848 / Rpim(I) all: 0.317 / Rsym value: 0.61 / % possible all: 99.8

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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: 3F00

3f00


Resolution: 1.38→29.988 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.32
RfactorNum. reflection% reflection
Rfree0.1782 3938 3.72 %
Rwork0.1445 --
obs0.1457 53727 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.9 Å2
Refinement stepCycle: LAST / Resolution: 1.38→29.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 12 353 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072116
X-RAY DIFFRACTIONf_angle_d1.082861
X-RAY DIFFRACTIONf_dihedral_angle_d13.071790
X-RAY DIFFRACTIONf_chiral_restr0.075307
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.39690.26571190.28453125X-RAY DIFFRACTION84
1.3969-1.41460.32551240.27623172X-RAY DIFFRACTION85
1.4146-1.43320.26651400.23213573X-RAY DIFFRACTION98
1.4332-1.45280.23771440.2063666X-RAY DIFFRACTION100
1.4528-1.47360.24971400.19353720X-RAY DIFFRACTION100
1.4736-1.49550.20691520.18863697X-RAY DIFFRACTION100
1.4955-1.51890.21971440.17823693X-RAY DIFFRACTION100
1.5189-1.54380.2191440.17313720X-RAY DIFFRACTION100
1.5438-1.57040.19611520.15983771X-RAY DIFFRACTION100
1.5704-1.5990.18341360.15763618X-RAY DIFFRACTION100
1.599-1.62970.1721440.15113704X-RAY DIFFRACTION100
1.6297-1.6630.17341320.14343754X-RAY DIFFRACTION100
1.663-1.69920.20591520.13993676X-RAY DIFFRACTION100
1.6992-1.73870.18171400.13623650X-RAY DIFFRACTION100
1.7387-1.78220.15951360.12913730X-RAY DIFFRACTION100
1.7822-1.83030.19391480.13153706X-RAY DIFFRACTION100
1.8303-1.88420.16111480.1293646X-RAY DIFFRACTION100
1.8842-1.9450.16821400.1253727X-RAY DIFFRACTION100
1.945-2.01450.17261440.12993658X-RAY DIFFRACTION100
2.0145-2.09510.17211280.13153682X-RAY DIFFRACTION100
2.0951-2.19050.20881560.13333740X-RAY DIFFRACTION100
2.1905-2.30590.1811340.13783709X-RAY DIFFRACTION100
2.3059-2.45030.15031400.13673627X-RAY DIFFRACTION99
2.4503-2.63940.20581420.14253695X-RAY DIFFRACTION99
2.6394-2.90480.16671490.1513609X-RAY DIFFRACTION98
2.9048-3.32470.16861370.14843609X-RAY DIFFRACTION98
3.3247-4.1870.17221380.12853650X-RAY DIFFRACTION98
4.187-29.99530.131350.13513528X-RAY DIFFRACTION95

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