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- PDB-7atp: 2.0 angstrom structure in complex with Ca of plant Extended Synap... -

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Basic information

Entry
Database: PDB / ID: 7atp
Title2.0 angstrom structure in complex with Ca 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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9195
Polymers16,7381
Non-polymers1814
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-68 kcal/mol
Surface area7660 Å2
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)50,75815
Polymers50,2153
Non-polymers54312
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 area4190 Å2
ΔGint-169 kcal/mol
Surface area19550 Å2
MethodPISA; in crystal form in presence of Zn or Cd/Ni
Unit cell
Length a, b, c (Å)69.127, 69.127, 115.669
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-403-

CL

21A-404-

ZN

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v Polyethylene glycol 6,000, 100 mM TRIS pH 8.0 and 10 mM Zinc chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→41.59 Å / Num. obs: 12025 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 1.712 / Num. unique obs: 988 / CC1/2: 0.55

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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: 2.1→41.59 Å / SU ML: 0.3334 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 39.1463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 1206 5.02 %
Rwork0.207 22804 -
obs0.21 12019 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 4 10 1068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951076
X-RAY DIFFRACTIONf_angle_d0.94791446
X-RAY DIFFRACTIONf_chiral_restr0.0528159
X-RAY DIFFRACTIONf_plane_restr0.0087182
X-RAY DIFFRACTIONf_dihedral_angle_d24.9004422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.38881020.35752530X-RAY DIFFRACTION99.77
2.18-2.280.32231600.33022549X-RAY DIFFRACTION99.89
2.28-2.40.36651220.31512555X-RAY DIFFRACTION99.96
2.4-2.560.26351580.26332510X-RAY DIFFRACTION100
2.56-2.750.34541180.25542541X-RAY DIFFRACTION99.96
2.75-3.030.30711340.31412513X-RAY DIFFRACTION99.96
3.03-3.470.31141440.24662568X-RAY DIFFRACTION99.78
3.47-4.370.23741500.18222485X-RAY DIFFRACTION99.89
4.37-41.590.24011180.15282553X-RAY DIFFRACTION99.52
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)
12.52385135352-1.140906333470.5707445005671.37878129627-1.02584776591.681003385610.10732200794-0.329633554737-0.1632270154650.3010004578310.4731180014220.3629734040450.84572650411-0.9430685456640.2041612170490.403608621640.05400875934520.09289710648970.7887331763320.01602804237070.634669300059-12.42001273711.852409489699.3896313146
22.356888410850.1904539454410.3910898698370.666901444250.239197309042.03948248236-0.190502270628-0.5675780514030.05720553364370.184971179790.4002591531080.107518967523-0.222035835396-0.5331113815170.02026821296510.4621493441360.1768304320830.04011105005730.6913865076050.04074519373140.507132163858-11.92585384378.0967743653110.9732345232
30.07321881587940.05042646228020.06413410339480.10637004528-0.02034276385450.1349859169020.02807469318740.5883280999960.564548838182-0.7219386926840.8998648488120.305899494706-1.434796220570.004335417056210.003813441520540.756548362990.143100897072-0.04160077839180.8382592102330.08097637407150.533169639723-7.033913736423.40409520556-5.94382395699
40.3581168980460.4127708174190.003732969027111.19498726783-0.8649684290480.6786745753170.117087588113-0.750387434784-0.361770124170.304976298478-0.1289806198780.7197396199230.0735002100924-1.163098399320.0542286833890.6126665383310.2062346710470.1277404466661.451971712620.09886116415490.876386278622-19.12892574926.8006888343516.9674877377
50.603235364792-0.497257099775-0.1031743356850.4073970517920.04529171665121.65817717753-0.0892202236457-1.59900579413-0.3039191435020.1372148731170.04077683423070.9399622516510.191542869861-2.153297877080.1666693430240.5297988437180.1738284533330.2038046554581.44166641127-0.07408282774850.852957343572-19.53099332163.4826712139314.9260001337
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 257 through 282 )257 - 2821 - 26
22chain 'A' and (resid 283 through 332 )283 - 33227 - 76
33chain 'A' and (resid 333 through 339 )333 - 33977 - 83
44chain 'A' and (resid 340 through 357 )340 - 35784 - 101
55chain 'A' and (resid 358 through 394 )358 - 394102 - 129

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