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- PDB-8jly: Structure of nanobody in complex with alpha-synuclein peptide -

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Basic information

Entry
Database: PDB / ID: 8jly
TitleStructure of nanobody in complex with alpha-synuclein peptide
Components
  • Nanobody
  • alpha-synuclein peptide
KeywordsIMMUNE SYSTEM / Nanobody / Parkinson's disease / alpha-synuclein / Nanobody peptide complex
Function / homology
Function and homology information


regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / dopamine uptake involved in synaptic transmission / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / : / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / protein destabilization / negative regulation of protein kinase activity / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / ferrous iron binding / positive regulation of protein serine/threonine kinase activity / tau protein binding / PKR-mediated signaling / receptor internalization / : / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / response to lipopolysaccharide / amyloid fibril formation / molecular adaptor activity / lysosome / transcription cis-regulatory region binding / oxidoreductase activity / positive regulation of apoptotic process
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesCamelus dromedarius (Arabian camel)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsIslam, Z. / Kolatkar, P.R.
Funding supportQatar, 1items
OrganizationGrant numberCountry
Qatar FoundationQatar
CitationJournal: Protein Sci. / Year: 2024
Title: Structural insights into the unique recognition module between alpha-synuclein peptide and nanobody.
Authors: Islam, Z. / Vaikath, N.N. / Hmila, I. / El-Agnaf, O.M.A. / Kolatkar, P.R.
History
DepositionJun 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
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

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Assembly

Deposited unit
A: Nanobody
B: alpha-synuclein peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4923
Polymers15,4002
Non-polymers921
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-7 kcal/mol
Surface area5890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.474, 41.906, 86.352
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-306-

HOH

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Components

#1: Antibody Nanobody


Mass: 14001.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide alpha-synuclein peptide


Mass: 1398.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P37840
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.76 Å3/Da / Density % sol: 30.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate trihydrate pH 4.6, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.25→28.5 Å / Num. obs: 30998 / % possible obs: 99.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 17.16 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 1.25→1.28 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 2028 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→28.5 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.6267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 2838 9.91 %
Rwork0.1609 25800 -
obs0.1633 28638 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.51 Å2
Refinement stepCycle: LAST / Resolution: 1.29→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 6 91 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051980
X-RAY DIFFRACTIONf_angle_d0.84541344
X-RAY DIFFRACTIONf_chiral_restr0.0874157
X-RAY DIFFRACTIONf_plane_restr0.0066172
X-RAY DIFFRACTIONf_dihedral_angle_d7.0725155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.310.29231420.24721241X-RAY DIFFRACTION97.81
1.31-1.330.26481500.2151244X-RAY DIFFRACTION99.36
1.33-1.360.24841330.20431272X-RAY DIFFRACTION99.36
1.36-1.390.2471430.19441270X-RAY DIFFRACTION99.65
1.39-1.420.22941340.18371262X-RAY DIFFRACTION99.5
1.42-1.450.19911480.15131291X-RAY DIFFRACTION99.93
1.45-1.490.19181420.15581242X-RAY DIFFRACTION99.35
1.49-1.530.18761520.14871279X-RAY DIFFRACTION99.1
1.53-1.570.1851320.1471277X-RAY DIFFRACTION99.79
1.57-1.620.18411270.15251302X-RAY DIFFRACTION99.86
1.62-1.680.21651360.16081289X-RAY DIFFRACTION99.58
1.68-1.750.18691300.14681279X-RAY DIFFRACTION99.72
1.75-1.830.18261440.14521282X-RAY DIFFRACTION99.79
1.83-1.920.16971620.14271271X-RAY DIFFRACTION99.79
1.92-2.050.17031410.13261292X-RAY DIFFRACTION99.93
2.05-2.20.17491520.14131285X-RAY DIFFRACTION100
2.2-2.420.17311300.15381316X-RAY DIFFRACTION99.93
2.42-2.770.19681450.17721348X-RAY DIFFRACTION100
2.78-3.50.17861380.15911342X-RAY DIFFRACTION100
3.5-100.17991570.1731416X-RAY DIFFRACTION99.62

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