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- PDB-7as6: 2.0 angstrom structure of plant Extended Synaptotagmin 1, C2A domain -

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Basic information

Entry
Database: PDB / ID: 7as6
Title2.0 angstrom structure of plant Extended Synaptotagmin 1, C2A domain
ComponentsSynaptotagmin-1
KeywordsLIPID BINDING PROTEIN / C2 domain / Beta Sandwich / lipid transport / contact sites
Function / homology
Function and homology information


lipid transport / endocytosis / endosome membrane / lipid binding / metal ion binding / plasma membrane
Similarity search - Function
Synaptotagmin, plant / Synaptotagmin, SMP domain / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
: / NICKEL (II) ION / Synaptotagmin-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBenavente, J.L. / Albert, A.
CitationJournal: Life Sci Alliance / Year: 2021
Title: The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites.
Authors: Benavente, J.L. / Siliqi, D. / Infantes, L. / Lagartera, L. / Mills, A. / Gago, F. / Ruiz-Lopez, N. / Botella, M.A. / Sanchez-Barrena, M.J. / Albert, A.
History
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,2408
Polymers16,7381
Non-polymers5027
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, In solution the protein is present as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration; in solution
2
A: Synaptotagmin-1
hetero molecules

A: Synaptotagmin-1
hetero molecules

A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,72024
Polymers50,2153
Non-polymers1,50521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5260 Å2
ΔGint-71 kcal/mol
Surface area21110 Å2
MethodPISA; in crystal form in presence of Zn or Cd/Ni
Unit cell
Length a, b, c (Å)70.937, 70.937, 116.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-402-

CD

21A-528-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Synaptotagmin-1 / NTMC2T1.1 / Synaptotagmin A / Extended Synaptotagmin 1 / C2A domain


Mass: 16738.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SYT1, SYTA, At2g20990, F26H11.25, F5H14.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SKR2

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Non-polymers , 5 types, 35 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% w/v Polyethylene glycol 3350, 100 mM HEPES pH 7.5, 5 mM Cobalt (II) chloride hexahydrate, 5 mM Nickel (II) chloride hexahydrate, 5 mM Cadmium chloride hydrate and 5 mM Magnesium chloride hexahydrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979178 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979178 Å / Relative weight: 1
ReflectionResolution: 2→42.233 Å / Num. obs: 14603 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.06 Å / Rmerge(I) obs: 1.664 / Num. unique obs: 1073 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANK

6ank


Resolution: 2→42.23 Å / SU ML: 0.2115 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.4567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2106 740 5.08 %
Rwork0.186 13833 -
obs0.1872 14573 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.98 Å2
Refinement stepCycle: LAST / Resolution: 2→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 13 28 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761102
X-RAY DIFFRACTIONf_angle_d0.91071476
X-RAY DIFFRACTIONf_chiral_restr0.0533161
X-RAY DIFFRACTIONf_plane_restr0.0071186
X-RAY DIFFRACTIONf_dihedral_angle_d21.5031434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.160.35061310.34272788X-RAY DIFFRACTION98.98
2.16-2.380.28171440.262758X-RAY DIFFRACTION99.52
2.38-2.720.24391590.22252769X-RAY DIFFRACTION99.69
2.72-3.430.21941780.18912734X-RAY DIFFRACTION99.66
3.43-42.230.17021280.15132784X-RAY DIFFRACTION98.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67077613270.307844478298-0.02629844880010.419940599828-0.1510273322920.3487429197590.0454821995433-0.005027647326320.04141558532570.0253317708087-0.1266766321840.449743792047-0.0443087311252-0.7007950512340.02515536717450.4279721849960.02017753814710.0472741484380.513287256378-0.005026070815660.451004687334-13.60554965474.3741113177311.9104660379
20.5426279513260.0552054003464-0.08894059979250.1888251181060.3386018876710.598589729076-0.0487948341112-0.01170239533830.1239860745070.6814065161390.347151961440.1313045361660.0874206771952-0.141128641330.002965002653750.3770578991260.03315541458070.0639887258520.3822779363050.009861332611130.428131199344-10.33587606484.7267979374411.123973761
30.853095121421-0.2419780648940.1302815367930.63426160987-0.1856747598830.4839308652610.0415832667860.09514094782340.282449661208-0.1153595276180.1045935442170.0564088018119-0.567729389885-0.197221350348-7.83377074777E-50.4036865753270.0714672284730.03492061650340.5272568791350.0284630534410.406744375436-16.37207586299.0977780148312.3246753204
40.274649030228-0.4051256788680.01104541231540.7865828484850.2168541728950.2932699495670.000365251809211-0.3147578102890.04990076202570.4000005852290.0778781210770.506654305702-0.0290669257918-0.9991066161060.04761044823620.4607137549310.06012524601240.07635722888540.780402569737-0.001268868459010.543006304064-20.32211248034.5432573678919.9222536051
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 256 through 289 )256 - 2891 - 34
22chain 'A' and (resid 290 through 311 )290 - 31135 - 56
33chain 'A' and (resid 312 through 351 )312 - 35157 - 96
44chain 'A' and (resid 352 through 395 )352 - 39597 - 131

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