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- PDB-7tx9: Human Synaptotagmin-1 C2B Y312F Ca2+ bound -

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Basic information

Entry
Database: PDB / ID: 7tx9
TitleHuman Synaptotagmin-1 C2B Y312F Ca2+ bound
ComponentsSynaptotagmin
KeywordsEXOCYTOSIS / C2 domain / AD3 / C2B / Greek Key / synaptotagmin
Function / homology
Function and homology information


chromaffin granule membrane / positive regulation of dendrite extension / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium ion binding
Similarity search - Function
Synaptotagmin / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Chem-1PG / Synaptotagmin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsDominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1R21MH070589-01 United States
CitationJournal: Biophys.J. / Year: 2024
Title: The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability.
Authors: Dominguez, M.J. / Bui, A.A. / Villarreal, J. / Snow, A. / Karmakar, S. / Harsini, F.M. / Rock, P.J. / Rice, A.M. / Fuson, K.L. / Sutton, R.B.
History
DepositionFeb 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4349
Polymers17,8641
Non-polymers5708
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.290, 54.290, 102.300
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

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Protein , 1 types, 1 molecules A

#1: Protein Synaptotagmin


Mass: 17863.818 Da / Num. of mol.: 1 / Fragment: UNP Residues 269-419 / Mutation: Y312F
Source method: isolated from a genetically manipulated source
Details: orginally cloned from human brain cDNA library / Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SYT1, hCG_2016754 / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J3KQA0

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate pH 4.5,200 mM ammonium sulfate, 50% w/v PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.09717 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09717 Å / Relative weight: 1
ReflectionResolution: 1.34→34.61 Å / Num. obs: 38659 / % possible obs: 96.38 % / Redundancy: 14.4 % / Biso Wilson estimate: 14.95 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06678 / Rpim(I) all: 0.01733 / Rrim(I) all: 0.06914 / Net I/σ(I): 24.3
Reflection shellResolution: 1.34→1.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3196 / CC1/2: 0.407 / CC star: 0.761 / Rpim(I) all: 0.8528 / Rrim(I) all: 1.519 / % possible all: 80.61

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
xia2data reduction
xia2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tz3

6tz3


Resolution: 1.34→34.61 Å / SU ML: 0.1802 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 2004 5.2 %
Rwork0.1693 36540 -
obs0.1703 38544 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.34→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 28 120 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921360
X-RAY DIFFRACTIONf_angle_d1.20131846
X-RAY DIFFRACTIONf_chiral_restr0.0864202
X-RAY DIFFRACTIONf_plane_restr0.0059235
X-RAY DIFFRACTIONf_dihedral_angle_d16.0316531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.37431110.37192085X-RAY DIFFRACTION77.96
1.37-1.410.37131300.35952398X-RAY DIFFRACTION89.74
1.41-1.450.34251380.32622599X-RAY DIFFRACTION97.3
1.45-1.50.25081480.24372642X-RAY DIFFRACTION99.32
1.5-1.550.26781500.2412637X-RAY DIFFRACTION98.38
1.55-1.610.32311340.31422542X-RAY DIFFRACTION95.13
1.61-1.690.18281460.16022689X-RAY DIFFRACTION99.96
1.69-1.780.26491370.23492511X-RAY DIFFRACTION93.5
1.78-1.890.16811510.13092676X-RAY DIFFRACTION99.61
1.89-2.030.17791470.1422670X-RAY DIFFRACTION99.02
2.03-2.240.12791530.10752722X-RAY DIFFRACTION99.9
2.24-2.560.16171450.11962739X-RAY DIFFRACTION99.79
2.56-3.230.1611530.15112738X-RAY DIFFRACTION99.48
3.23-34.610.1711610.16252892X-RAY DIFFRACTION99.77

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