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- PDB-2r83: Crystal structure analysis of human synaptotagmin 1 C2A-C2B -

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Basic information

Entry
Database: PDB / ID: 2r83
TitleCrystal structure analysis of human synaptotagmin 1 C2A-C2B
ComponentsSynaptotagmin-1
KeywordsENDOCYTOSIS / EXOCYTOSIS / C2A-C2B / Calcium / Cell junction / Cytoplasmic vesicle / Glycoprotein / Lipoprotein / Membrane / Metal-binding / Palmitate / Phosphorylation / Synapse / Transmembrane / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / 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 / calcium ion sensor activity / regulation of regulated secretory pathway ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / 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 / calcium ion sensor activity / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / clathrin-sculpted monoamine transport vesicle membrane / dense core granule / chromaffin granule membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / positive regulation of dendrite extension / regulation of exocytosis / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / syntaxin binding / low-density lipoprotein particle receptor binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / cellular response to calcium ion / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / SNARE binding / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSutton, R.B. / Fuson, K.L. / Montes, M. / Robert, J.J.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of human synaptotagmin 1 C2AB in the absence of Ca2+ reveals a novel domain association.
Authors: Fuson, K.L. / Montes, M. / Robert, J.J. / Sutton, R.B.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 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 / 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 / _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-1
B: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,35310
Polymers65,0692
Non-polymers2848
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.372, 86.310, 147.186
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: 32534.469 Da / Num. of mol.: 2 / Fragment: C2A-C2B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Plasmid: PGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4.08 Å3/Da / Density % sol: 69.87 %
Crystal growpH: 4.5
Details: 3M NACL, 75 MM SODIUM ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 29346 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
ADSCdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RSY, PDB ENTRY 1TJX

1rsy

1tjx


Resolution: 2.7→46.31 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1245461.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2921 10 %RANDOM
Rwork0.23 ---
obs0.23 29304 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.67 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-9.69 Å20 Å20 Å2
2--0.91 Å20 Å2
3----10.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 8 43 4565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 472 9.8 %
Rwork0.354 4361 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.PARAM
X-RAY DIFFRACTION3ION.PARAMWATER.PARAM

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