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- PDB-8og0: Crystal structure of MJF14-6-4-2 Fab fragment in complex with epi... -

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Basic information

Entry
Database: PDB / ID: 8og0
TitleCrystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide
Components
  • Alpha-synuclein
  • Fab fragment heavy chainFragment antigen-binding
  • Fab fragment light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Alpha synuclein / Fab fragment / MJF14-6-4-2 / epitope
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / dopamine biosynthetic process / SNARE complex assembly / positive regulation of neurotransmitter secretion / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / regulation of macrophage activation / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / mitochondrial ATP synthesis coupled electron transport / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / positive regulation of endocytosis / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / kinesin binding / alpha-tubulin binding / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / cellular response to epinephrine stimulus / excitatory postsynaptic potential / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / regulation of transmembrane transporter activity / ferrous iron binding / synapse organization / phospholipid binding / protein tetramerization / phosphoprotein binding / microglial cell activation / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / tau protein binding / protein destabilization / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / receptor internalization / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / actin binding / cell cortex / histone binding / growth cone / chemical synaptic transmission / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / lysosome / molecular adaptor activity / oxidoreductase activity / transcription cis-regulatory region binding
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 Å
AuthorsTars, K. / Lieknina, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)OligoFITEuropean Union
CitationJournal: To be published
Title: Structural basis of epitope recognition by anti-alpha synuclein antibodies MJF14-6-4-2
Authors: Tars, K. / Lieknina, I.
History
DepositionMar 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab fragment light chain
H: Fab fragment heavy chain
P: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)46,8653
Polymers46,8653
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area18250 Å2
Unit cell
Length a, b, c (Å)37.484, 66.700, 167.167
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: Antibody Fab fragment light chain / Fragment antigen-binding


Mass: 22771.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit)
#2: Antibody Fab fragment heavy chain / Fragment antigen-binding


Mass: 23486.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit)
#3: Protein/peptide Alpha-synuclein / / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 607.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P37840
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Sitting droplets were set up by mixing 1 ul of Fab fragments, 0.5 ul of peptide (1 mg/ml in 20 mM tris-HCl) and 1 ul crystallization buffer (24% PEG 6000, 0.1M Na-citrate pH 5.0).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.712→83.58 Å / Num. obs: 37216 / % possible obs: 94.3 % / Redundancy: 13 % / Rmerge(I) obs: 0.208 / Net I/σ(I): 8.5
Reflection shellResolution: 1.712→1.902 Å / Rmerge(I) obs: 1.609 / Num. unique obs: 1626

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCv1.0.5data reduction
autoPROCv1.0.5data scaling
PHASERv2.5.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.712→83.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.525 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23117 1594 4.9 %RANDOM
Rwork0.19531 ---
obs0.19704 30930 70.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0 Å2
2--0.16 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.712→83.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 171 3382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0113360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162927
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.654617
X-RAY DIFFRACTIONr_angle_other_deg0.4771.5476848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6555445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.766510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48710483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02662
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9362.3991768
X-RAY DIFFRACTIONr_mcbond_other1.9352.3991768
X-RAY DIFFRACTIONr_mcangle_it2.9373.582217
X-RAY DIFFRACTIONr_mcangle_other2.9363.582218
X-RAY DIFFRACTIONr_scbond_it2.1892.4891592
X-RAY DIFFRACTIONr_scbond_other2.1882.4881593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2663.6662401
X-RAY DIFFRACTIONr_long_range_B_refined4.70231.3753563
X-RAY DIFFRACTIONr_long_range_B_other4.65130.933540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.712→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 9 -
Rwork0.309 136 -
obs--4.37 %

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