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- PDB-5ccj: Crystal structure of the quintuple mutant of the synaptotagmin-1 ... -

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Basic information

Entry
Database: PDB / ID: 5ccj
TitleCrystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain
ComponentsSynaptotagmin-1
KeywordsSIGNALING PROTEIN / Synaptotagmin1 / C2B domain
Function / homology
Function and homology information


regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane ...regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / exocytic vesicle / positive regulation of calcium ion-dependent exocytosis / vesicle organization / protein heterooligomerization / positive regulation of dendrite extension / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / positive regulation of dopamine secretion / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / vesicle fusion / dense core granule / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / neurotransmitter secretion / syntaxin binding / presynaptic active zone / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / synaptic vesicle exocytosis / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / postsynaptic cytosol / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / secretory granule / hippocampal mossy fiber to CA3 synapse / SNARE binding / molecular condensate scaffold activity / response to calcium ion / phospholipid binding / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / presynaptic membrane / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / calcium ion binding / lipid binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsZhou, Q. / Zhao, M. / Brunger, A.T.
CitationJournal: Nature / Year: 2015
Title: Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis.
Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. ...Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. / Lemke, H.T. / Pfuetzner, R.A. / Choi, U.B. / Weis, W.I. / Diao, J. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: Synaptotagmin-1
D: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,67153
Polymers68,0714
Non-polymers4,60049
Water13,836768
1
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,05112
Polymers17,0181
Non-polymers1,03311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,43116
Polymers17,0181
Non-polymers1,41315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,85910
Polymers17,0181
Non-polymers8419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,33115
Polymers17,0181
Non-polymers1,31314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-317 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.920, 107.590, 110.800
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: 17017.801 Da / Num. of mol.: 4 / Fragment: UNP residues 271-421 / Mutation: R281A, E295A, Y338W, R398A, R399A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 98593 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 19.69 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.99
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 2.34 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.55 Å77.19 Å
Translation7.55 Å77.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOW

1uow


Resolution: 1.65→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 4930 5 %
Rwork0.15 --
obs0.151 98587 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 272 768 5719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195402
X-RAY DIFFRACTIONf_angle_d1.7637356
X-RAY DIFFRACTIONf_dihedral_angle_d13.2022013
X-RAY DIFFRACTIONf_chiral_restr0.116811
X-RAY DIFFRACTIONf_plane_restr0.01909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66870.33161590.26773032X-RAY DIFFRACTION98
1.6687-1.68830.23091630.24163084X-RAY DIFFRACTION98
1.6883-1.70890.26451620.21573074X-RAY DIFFRACTION98
1.7089-1.73060.23151610.20023076X-RAY DIFFRACTION98
1.7306-1.75330.24671620.19413070X-RAY DIFFRACTION99
1.7533-1.77740.21051620.18013077X-RAY DIFFRACTION99
1.7774-1.80280.25031620.17673080X-RAY DIFFRACTION99
1.8028-1.82970.21931620.17013082X-RAY DIFFRACTION99
1.8297-1.85830.19721640.16363116X-RAY DIFFRACTION99
1.8583-1.88870.21261610.15543053X-RAY DIFFRACTION99
1.8887-1.92130.19881650.15813134X-RAY DIFFRACTION99
1.9213-1.95620.17941620.14383072X-RAY DIFFRACTION99
1.9562-1.99390.18251620.15183086X-RAY DIFFRACTION99
1.9939-2.03460.19881650.15533133X-RAY DIFFRACTION99
2.0346-2.07880.16951630.14163089X-RAY DIFFRACTION99
2.0788-2.12720.1811620.14493092X-RAY DIFFRACTION99
2.1272-2.18040.17161640.14483104X-RAY DIFFRACTION99
2.1804-2.23930.16741650.14633135X-RAY DIFFRACTION99
2.2393-2.30520.16311650.14433130X-RAY DIFFRACTION99
2.3052-2.37960.15371640.14483124X-RAY DIFFRACTION99
2.3796-2.46470.17791650.1433136X-RAY DIFFRACTION99
2.4647-2.56340.191650.14893145X-RAY DIFFRACTION100
2.5634-2.680.18071650.15353127X-RAY DIFFRACTION100
2.68-2.82130.17921650.15113124X-RAY DIFFRACTION99
2.8213-2.99810.18251660.15683171X-RAY DIFFRACTION99
2.9981-3.22960.17541670.14643160X-RAY DIFFRACTION100
3.2296-3.55460.1621670.13283183X-RAY DIFFRACTION99
3.5546-4.0690.1541690.13113200X-RAY DIFFRACTION99
4.069-5.12630.13971680.12073206X-RAY DIFFRACTION99
5.1263-77.27210.18531780.17013362X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.0053 Å / Origin y: -1.7077 Å / Origin z: -17.8569 Å
111213212223313233
T0.0974 Å2-0.0119 Å20.0024 Å2-0.1014 Å20.0017 Å2--0.1184 Å2
L0.1648 °2-0.0379 °2-0.0135 °2-0.1462 °2-0.0741 °2--0.4979 °2
S-0.0192 Å °-0.0211 Å °-0.0102 Å °-0.0143 Å °-0.0198 Å °-0.0209 Å °0.011 Å °-0.0053 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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