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- PDB-6u41: 1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G) -

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Basic information

Entry
Database: PDB / ID: 6u41
Title1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G)
ComponentsSynaptotagmin-1
KeywordsEXOCYTOSIS / C2 domain / C2B / Greek Key
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway ...clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / 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 / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / 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: 1.7 Å
AuthorsDominguez, M.J. / Bradberry, M.M. / Chapman, E.R. / Sutton, R.B.
CitationJournal: Neuron / Year: 2020
Title: Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.
Authors: Bradberry, M.M. / Courtney, N.A. / Dominguez, M.J. / Lofquist, S.M. / Knox, A.T. / Sutton, R.B. / Chapman, E.R.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3026
Polymers17,8221
Non-polymers4805
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.290, 54.290, 103.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 17821.783 Da / Num. of mol.: 1 / Mutation: D304G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SYT1, SVP65, SYT / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.0 M Ammonium Sulfate, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98397 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 1.7→34.6 Å / Num. obs: 20049 / % possible obs: 99.7 % / Redundancy: 18.4 % / Biso Wilson estimate: 14.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.039 / Net I/σ(I): 50.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 12 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 15 / Num. unique obs: 935 / CC1/2: 0.992 / Rrim(I) all: 0.141 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB-REDOrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOW

1uow


Resolution: 1.7→34.59 Å / SU ML: 0.1242 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 16.6924
RfactorNum. reflection% reflection
Rfree0.1783 1085 5.42 %
Rwork0.1569 --
obs0.1581 20014 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 25 192 1396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821410
X-RAY DIFFRACTIONf_angle_d0.85061926
X-RAY DIFFRACTIONf_chiral_restr0.0593209
X-RAY DIFFRACTIONf_plane_restr0.0054248
X-RAY DIFFRACTIONf_dihedral_angle_d17.657553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.780.20321320.15962240X-RAY DIFFRACTION97.05
1.78-1.870.22071220.15412363X-RAY DIFFRACTION99.96
1.87-1.990.17821210.14842355X-RAY DIFFRACTION99.96
1.99-2.140.15171210.14692354X-RAY DIFFRACTION100
2.14-2.360.18211790.14332333X-RAY DIFFRACTION99.96
2.36-2.70.17491290.15492358X-RAY DIFFRACTION99.84
2.7-3.40.18071310.16792417X-RAY DIFFRACTION99.77
3.4-34.590.17281500.16132509X-RAY DIFFRACTION99.7

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