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- PDB-8jjv: Structure of truncated form of nanobody in complex with alpha-syn... -

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Basic information

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


negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / 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 / mitochondrial membrane organization ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / 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 / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / regulation of reactive oxygen species biosynthetic process / 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 / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / synaptic vesicle priming / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / kinesin binding / synaptic vesicle endocytosis / regulation of presynapse assembly / response to type II interferon / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / alpha-tubulin binding / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / phosphoprotein binding / protein tetramerization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / growth cone / cell cortex / cellular response to oxidative stress / neuron apoptotic process / chemical synaptic transmission / molecular adaptor activity / negative regulation of neuron apoptotic process / response to lipopolysaccharide / histone binding / amyloid fibril formation / lysosome / oxidoreductase activity / postsynapse / transcription cis-regulatory region binding / positive regulation of apoptotic process / Amyloid fiber formation / copper ion binding / response to xenobiotic stimulus / axon / neuronal cell body
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: 1.23 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
DepositionMay 31, 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 1.2Nov 20, 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
A: Nanobody
B: Alpha-synuclein peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5844
Polymers15,4002
Non-polymers1842
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-8 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.346, 41.618, 85.032
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)
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-324-

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 / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.74 Å3/Da / Density % sol: 29.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS pH 5.5, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 31814 / % possible obs: 98.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 14.98 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 1.23→1.26 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 2048 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→30 Å / SU ML: 0.1304 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.3805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 3183 10.02 %RANDOM
Rwork0.1423 28579 --
obs0.1452 31762 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.06 Å2
Refinement stepCycle: LAST / Resolution: 1.23→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 12 129 1041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055997
X-RAY DIFFRACTIONf_angle_d0.88281357
X-RAY DIFFRACTIONf_chiral_restr0.0896155
X-RAY DIFFRACTIONf_plane_restr0.0103172
X-RAY DIFFRACTIONf_dihedral_angle_d9.5015159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.27251210.27081004X-RAY DIFFRACTION83.71
1.25-1.270.26771290.24611162X-RAY DIFFRACTION92.74
1.27-1.290.27841240.20471204X-RAY DIFFRACTION97.15
1.29-1.310.23581410.17991206X-RAY DIFFRACTION98.54
1.31-1.330.19191440.15931234X-RAY DIFFRACTION99.93
1.33-1.360.1921330.13711234X-RAY DIFFRACTION100
1.36-1.390.17561450.13031261X-RAY DIFFRACTION99.93
1.39-1.420.18361430.13161208X-RAY DIFFRACTION100
1.42-1.450.15991350.1251253X-RAY DIFFRACTION100
1.45-1.490.16641430.12061232X-RAY DIFFRACTION100
1.49-1.530.1621330.12911266X-RAY DIFFRACTION100
1.53-1.570.15471250.12781245X-RAY DIFFRACTION100
1.57-1.620.15021510.11971239X-RAY DIFFRACTION100
1.62-1.680.19071380.13461268X-RAY DIFFRACTION100
1.68-1.750.16431350.13821243X-RAY DIFFRACTION100
1.75-1.830.16831280.131267X-RAY DIFFRACTION99.93
1.83-1.920.16831340.13151271X-RAY DIFFRACTION100
1.92-2.040.13731320.13121276X-RAY DIFFRACTION100
2.04-2.20.15131330.13711283X-RAY DIFFRACTION100
2.2-2.420.15851490.14271259X-RAY DIFFRACTION99.93
2.42-2.770.20341540.15881286X-RAY DIFFRACTION100
2.77-3.490.17551420.14271308X-RAY DIFFRACTION100
3.49-28.580.15691710.1411370X-RAY DIFFRACTION99.87

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