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- PDB-6cxw: Synaptotagmin 1 C2A beta4 chimera with enhanced PIP2 binding function -

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Basic information

Entry
Database: PDB / ID: 6cxw
TitleSynaptotagmin 1 C2A beta4 chimera with enhanced PIP2 binding function
ComponentsSynaptotagmin 1 C2A beta4 chimera
KeywordsEXOCYTOSIS / C2 domain
Function / homology
Function and homology information


synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / calcium-dependent phospholipid binding / neuron projection terminus / syntaxin-1 binding / syntaxin binding / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / 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 / secretory granule / phospholipid binding / terminal bouton / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.832 Å
AuthorsSutton, R.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)061876 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)063634 United States
CitationJournal: To Be Published
Title: Engineering a C2-domain to bind PIP2
Authors: Evans, C.S. / Lou, X. / Bai, H. / Rice, A.M. / Salcido-Holguin, L. / Rodriguez, E.N. / Sutton, R.B. / Chapman, E.R.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin 1 C2A beta4 chimera


Theoretical massNumber of molelcules
Total (without water)14,6931
Polymers14,6931
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.143, 45.105, 89.278
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Synaptotagmin 1 C2A beta4 chimera / Synaptotagmin I / SytI / p65


Mass: 14692.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8.5 / Details: 50% PEG-4000, 0.4 mM Sodium acetate, 100 mM Tris

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.283572 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2016 / Details: Rh coasted flat bent mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283572 Å / Relative weight: 1
ReflectionResolution: 1.83→31.73 Å / Num. obs: 9789 / % possible obs: 96.8 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.011 / Rrim(I) all: 0.036 / Net I/σ(I): 51.6 / Num. measured all: 85169 / Scaling rejects: 88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.83-1.872.50.06912214840.990.0480.08512.480.2
8.97-31.739.30.054865930.9990.0180.05778.289.5

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wee

4wee


Resolution: 1.832→31.728 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 977 10.01 %Random selection
Rwork0.1747 8786 --
obs0.1785 9763 95.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.79 Å2 / Biso mean: 24.2284 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: final / Resolution: 1.832→31.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 0 131 1156
Biso mean---30.12 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041054
X-RAY DIFFRACTIONf_angle_d0.7161421
X-RAY DIFFRACTIONf_chiral_restr0.049155
X-RAY DIFFRACTIONf_plane_restr0.005182
X-RAY DIFFRACTIONf_dihedral_angle_d15.397635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8322-1.92880.20991260.19371134126089
1.9288-2.04960.22041420.182712771419100
2.0496-2.20780.21391400.1721260140099
2.2078-2.42990.22861410.18031277141898
2.4299-2.78140.24921410.1961261140297
2.7814-3.50350.21751420.18031276141896
3.5035-31.73290.18011450.15381301144693
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)
12.2836-0.10711.19272.29160.02584.5117-0.00540.19650.0527-0.3268-0.02910.041-0.41850.38510.02920.11320.0147-0.00570.06470.01130.112311.14655.143-20.4413
22.6330.74311.14265.6503-0.8553.1585-0.1034-1.5807-0.3311.09190.2919-0.1058-0.11510.13870.24130.26970.0234-0.0370.46920.03870.154616.2053-0.92353.3708
35.87820.49835.02940.55320.43956.01920.0567-0.0269-0.1323-0.1316-0.0881-0.00790.20220.0569-0.22250.10130.01080.01350.0455-0.0050.10459.8583-5.7186-16.888
45.1421-0.12422.45810.98890.27352.49390.39060.1841-0.6907-0.12090.1145-0.18120.3759-0.1057-0.20440.1460.0379-0.0385-0.0075-0.03260.22497.4435-9.4767-21.9624
51.6387-0.12590.0532.16330.7342.3373-0.0095-0.0455-0.0157-0.1724-0.0507-0.1425-0.19460.2295-0.01650.0496-0.00540.00610.08040.02730.12218.73241.0698-13.5141
61.93650.2861-0.47981.43090.05432.27260.02840.13190.1368-0.3576-0.24290.06620.162-0.37830.02990.15870.0458-0.01130.0821-0.01590.11185.8159-2.2115-22.1834
70.9682-2.11920.50835.4906-1.17614.8103-0.2123-0.6586-0.05650.2340.1794-0.05830.01720.0148-0.01710.15240.0358-0.01130.18990.04630.116820.0579-13.1546-3.2038
82.7369-0.07741.11850.14260.12410.85830.00980.049-0.0976-0.02690.01280.09050.0746-0.1054-0.06070.08450.01510.0280.0856-0.01430.09113.68222.5098-18.1718
91.3541-0.33990.21581.9065-0.82663.10790.1257-0.14210.05030.14920.1980.5699-0.3473-0.2075-0.23760.08770.02450.01770.1360.03360.15725.18245.1034-10.6362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 141 through 166 )A141 - 166
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 178 )A167 - 178
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 187 )A179 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 196 )A188 - 196
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 215 )A197 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 232 )A216 - 232
7X-RAY DIFFRACTION7chain 'A' and (resid 233 through 239 )A233 - 239
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 257 )A240 - 257
9X-RAY DIFFRACTION9chain 'A' and (resid 258 through 267 )A258 - 267

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