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- PDB-8c5h: NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytoso... -

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Basic information

Entry
Database: PDB / ID: 8c5h
TitleNbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1
Components
  • NbSyt1 nanobody
  • Synaptotagmin-1
KeywordsMETAL BINDING PROTEIN / Nanobody / Synaptotagmin 1
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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMartinez-Carranza, M. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2022-03681 Sweden
CitationJournal: Small Methods / Year: 2023
Title: A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy.
Authors: Queiroz Zetune Villa Real, K. / Mougios, N. / Rehm, R. / Sograte-Idrissi, S. / Albert, L. / Rahimi, A.M. / Maidorn, M. / Hentze, J. / Martinez-Carranza, M. / Hosseini, H. / Saal, K.A. / ...Authors: Queiroz Zetune Villa Real, K. / Mougios, N. / Rehm, R. / Sograte-Idrissi, S. / Albert, L. / Rahimi, A.M. / Maidorn, M. / Hentze, J. / Martinez-Carranza, M. / Hosseini, H. / Saal, K.A. / Oleksiievets, N. / Prigge, M. / Tsukanov, R. / Stenmark, P. / Fornasiero, E.F. / Opazo, F.
History
DepositionJan 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
S: Synaptotagmin-1
N: NbSyt1 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4969
Polymers28,9032
Non-polymers5937
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-12 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.410, 65.750, 66.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Synaptotagmin I / SytI / p65


Mass: 15365.521 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 BL21(DE3) (bacteria) / References: UniProt: P21707
#2: Antibody NbSyt1 nanobody


Mass: 13537.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A51 anti rat synaptotagmin-1 nanobody / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Di-Malic acid pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.68→46.9 Å / Num. obs: 49689 / % possible obs: 97.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 31.06 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.85
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 3.822 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 1246 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Coot0.9.5model building
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T0R, 6I2G

5t0r

6i2g


Resolution: 1.68→41.26 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 2477 4.99 %
Rwork0.2091 --
obs0.2098 49687 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 37 46 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082028
X-RAY DIFFRACTIONf_angle_d0.9532732
X-RAY DIFFRACTIONf_dihedral_angle_d9.286282
X-RAY DIFFRACTIONf_chiral_restr0.057288
X-RAY DIFFRACTIONf_plane_restr0.01350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.40361320.39482510X-RAY DIFFRACTION94
1.71-1.750.42411310.36082560X-RAY DIFFRACTION95
1.75-1.790.37051250.35472569X-RAY DIFFRACTION96
1.79-1.830.36391510.34812616X-RAY DIFFRACTION97
1.83-1.870.36141400.32012631X-RAY DIFFRACTION97
1.87-1.920.34061410.28512589X-RAY DIFFRACTION97
1.92-1.980.29161400.2522612X-RAY DIFFRACTION97
1.98-2.040.21721340.23132612X-RAY DIFFRACTION98
2.04-2.120.27231320.22532653X-RAY DIFFRACTION98
2.12-2.20.25831360.21932635X-RAY DIFFRACTION98
2.2-2.30.23221400.2112627X-RAY DIFFRACTION98
2.3-2.420.18921360.20252639X-RAY DIFFRACTION98
2.42-2.570.21061480.21982644X-RAY DIFFRACTION99
2.57-2.770.26351350.2082655X-RAY DIFFRACTION98
2.77-3.050.25611450.20582647X-RAY DIFFRACTION99
3.05-3.490.20261370.18432665X-RAY DIFFRACTION99
3.49-4.40.14881370.17962667X-RAY DIFFRACTION99
4.4-41.260.21131370.18992679X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.8137 Å / Origin y: 9.3993 Å / Origin z: 8.6404 Å
111213212223313233
T0.1955 Å20.0043 Å2-0.0053 Å2-0.222 Å20.0304 Å2--0.2076 Å2
L1.0922 °20.0041 °2-0.2622 °2-3.5132 °21.7879 °2--2.5595 °2
S-0.0183 Å °0.0378 Å °-0.0342 Å °0.0392 Å °0.1048 Å °-0.0436 Å °-0.0374 Å °0.0526 Å °-0.1007 Å °
Refinement TLS groupSelection details: all

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