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- PDB-6xli: CRYSTAL STRUCTURE OF ANTI-TAU ANTIBODY PT3 Fab+pT212/pT217-TAU PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 6xli
TitleCRYSTAL STRUCTURE OF ANTI-TAU ANTIBODY PT3 Fab+pT212/pT217-TAU PEPTIDE
Components
  • PT3 Fab Heavy Chain
  • PT3 Fab Light Chain
  • Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / ANTIBODY / NEUROSCIENCE
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / lipoprotein particle binding / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / apolipoprotein binding / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / stress granule assembly / regulation of cellular response to heat / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / SH3 domain binding / cellular response to reactive oxygen species / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding
Similarity search - Function
: / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile.
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMalia, T.J. / Teplyakov, A. / Luo, J.
CitationJournal: J Alzheimers Dis / Year: 2020
Title: Discovery and Functional Characterization of hPT3, a Humanized Anti-Phospho Tau Selective Monoclonal Antibody.
Authors: Van Kolen, K. / Malia, T.J. / Theunis, C. / Nanjunda, R. / Teplyakov, A. / Ernst, R. / Wu, S.J. / Luo, J. / Borgers, M. / Vandermeeren, M. / Bottelbergs, A. / Wintmolders, C. / Lacy, E. / ...Authors: Van Kolen, K. / Malia, T.J. / Theunis, C. / Nanjunda, R. / Teplyakov, A. / Ernst, R. / Wu, S.J. / Luo, J. / Borgers, M. / Vandermeeren, M. / Bottelbergs, A. / Wintmolders, C. / Lacy, E. / Maurin, H. / Larsen, P. / Willems, R. / Van De Casteele, T. / Triana-Baltzer, G. / Slemmon, R. / Galpern, W. / Trojanowski, J.Q. / Sun, H. / Mercken, M.H.
History
DepositionJun 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: PT3 Fab Heavy Chain
B: PT3 Fab Light Chain
C: PT3 Fab Heavy Chain
D: PT3 Fab Light Chain
H: PT3 Fab Heavy Chain
L: PT3 Fab Light Chain
E: Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
F: Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
P: Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,37812
Polymers150,1019
Non-polymers2763
Water13,655758
1
A: PT3 Fab Heavy Chain
B: PT3 Fab Light Chain
E: Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1264
Polymers50,0343
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-36 kcal/mol
Surface area19660 Å2
MethodPISA
2
C: PT3 Fab Heavy Chain
D: PT3 Fab Light Chain
F: Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1264
Polymers50,0343
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-38 kcal/mol
Surface area19980 Å2
MethodPISA
3
H: PT3 Fab Heavy Chain
L: PT3 Fab Light Chain
P: Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1264
Polymers50,0343
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-38 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.240, 83.660, 166.870
Angle α, β, γ (deg.)90.000, 92.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PT3 Fab Heavy Chain


Mass: 24536.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody PT3 Fab Light Chain


Mass: 23870.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Tau Phosphopeptide (Ac-SR(pT)PSLP(pT)PPTRE-OH)


Mass: 1626.599 Da / Num. of mol.: 3
Fragment: residues 210-222 of Tau, phosporylated on T212 and T217
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M NH4H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.83 Å / Num. obs: 116430 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.09
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.555 / Num. unique obs: 8607

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I19

5i19


Resolution: 2→36.159 Å / Cross valid method: THROUGHOUT / σ(F): 1.36
RfactorNum. reflection% reflection
Rfree0.2133 2002 1.72 %
Rwork0.1858 --
obs0.1863 116414 99.25 %
Displacement parametersBiso max: 95.85 Å2 / Biso mean: 41.0952 Å2 / Biso min: 17.39 Å2
Refinement stepCycle: LAST / Resolution: 2→36.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10111 0 18 758 10887

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