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- PDB-8pii: VHH Z70 mutant 3 in interaction with PHF6 Tau peptide -

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Basic information

Entry
Database: PDB / ID: 8pii
TitleVHH Z70 mutant 3 in interaction with PHF6 Tau peptide
Components
  • Microtubule-associated protein tauTau protein
  • VHH Z70 Mutant 3
KeywordsIMMUNE SYSTEM / VHH / nanobody / complex / Tau
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 / 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 / lipoprotein particle binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / 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 / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / supramolecular fiber organization / stress granule assembly / regulation of cellular response to heat / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / axon cytoplasm / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / 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 / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cellular response to reactive oxygen species / microtubule cytoskeleton organization / SH3 domain binding / cytoplasmic ribonucleoprotein granule / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / cellular response to heat / cell body / protein-folding chaperone binding / growth cone / microtubule binding / double-stranded DNA binding / microtubule / sequence-specific DNA binding / amyloid fibril formation / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / 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 speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDupre, E. / Mortelecque, J. / NGuyen, M. / Hanoulle, X. / Landrieu, I.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE44-0016 France
Laboratories of Excellence (LabEx)ANR-11-LABX-01 France
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A selection and optimization strategy for single-domain antibodies targeting the PHF6 linear peptide within the tau intrinsically disordered protein.
Authors: Mortelecque, J. / Zejneli, O. / Begard, S. / Simoes, M.C. / ElHajjar, L. / Nguyen, M. / Cantrelle, F.X. / Hanoulle, X. / Rain, J.C. / Colin, M. / Gomes, C.M. / Buee, L. / Landrieu, I. / Danis, C. / Dupre, E.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Structure summary
Category: citation / pdbx_validate_planes / struct
Item: _citation.title / _pdbx_validate_planes.type / _struct.title
Revision 1.2Apr 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_planes
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_validate_planes.type
Revision 1.3Apr 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VHH Z70 Mutant 3
B: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)15,2052
Polymers15,2052
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-8 kcal/mol
Surface area6760 Å2
Unit cell
Length a, b, c (Å)135.435, 135.435, 35.425
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody VHH Z70 Mutant 3


Mass: 13744.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Microtubule-associated protein tau / Tau protein / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1460.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.09 Å3/Da / Density % sol: 60.18 % / Description: hexagonal rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M ammonium sulfate, 4.5% isopropanol, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→44.33 Å / Num. obs: 8432 / % possible obs: 100 % / Redundancy: 38.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.045 / Rrim(I) all: 0.208 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.1-44.3329.50.0581870.9990.0130.06
2.35-2.4340.22.2277890.9470.492.281

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
REFMAC5.8.0415refinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→44.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.729 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.217
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2632 398 4.728 %
Rwork0.2003 8020 -
all0.203 --
obs-8418 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.058 Å2
Baniso -1Baniso -2Baniso -3
1-1.119 Å20.559 Å20 Å2
2--1.119 Å20 Å2
3----3.629 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 0 30 946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011941
X-RAY DIFFRACTIONr_bond_other_d0.0010.016837
X-RAY DIFFRACTIONr_angle_refined_deg1.391.6641270
X-RAY DIFFRACTIONr_angle_other_deg0.4991.5711925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2825120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.30255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16410143
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3771041
X-RAY DIFFRACTIONr_chiral_restr0.0690.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02236
X-RAY DIFFRACTIONr_nbd_refined0.1990.2134
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.2717
X-RAY DIFFRACTIONr_nbtor_refined0.190.2447
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.210
X-RAY DIFFRACTIONr_nbd_other0.1690.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0670.24
X-RAY DIFFRACTIONr_mcbond_it4.2794.21486
X-RAY DIFFRACTIONr_mcbond_other4.2844.211486
X-RAY DIFFRACTIONr_mcangle_it6.4517.51604
X-RAY DIFFRACTIONr_mcangle_other6.4487.513605
X-RAY DIFFRACTIONr_scbond_it5.254.614455
X-RAY DIFFRACTIONr_scbond_other5.2454.618456
X-RAY DIFFRACTIONr_scangle_it7.8178.214666
X-RAY DIFFRACTIONr_scangle_other7.8128.216667
X-RAY DIFFRACTIONr_lrange_it10.0440.028989
X-RAY DIFFRACTIONr_lrange_other10.03940.039989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.249290.249562X-RAY DIFFRACTION100
2.411-2.4770.365260.255563X-RAY DIFFRACTION100
2.477-2.5480.258270.246564X-RAY DIFFRACTION100
2.548-2.6260.299320.225509X-RAY DIFFRACTION100
2.626-2.7120.223290.196518X-RAY DIFFRACTION100
2.712-2.8070.322290.198487X-RAY DIFFRACTION100
2.807-2.9130.258180.195492X-RAY DIFFRACTION100
2.913-3.0310.254250.207467X-RAY DIFFRACTION100
3.031-3.1650.33220.202449X-RAY DIFFRACTION100
3.165-3.3190.237140.188438X-RAY DIFFRACTION100
3.319-3.4970.25230.188420X-RAY DIFFRACTION100
3.497-3.7080.285170.181385X-RAY DIFFRACTION100
3.708-3.9620.175180.186377X-RAY DIFFRACTION100
3.962-4.2770.331140.177349X-RAY DIFFRACTION100
4.277-4.680.184200.155322X-RAY DIFFRACTION100
4.68-5.2260.173190.168292X-RAY DIFFRACTION100
5.226-6.020.26110.224272X-RAY DIFFRACTION100
6.02-7.3390.80590.258235X-RAY DIFFRACTION100
7.339-10.240.38460.217193X-RAY DIFFRACTION100
10.24-44.330.264100.306126X-RAY DIFFRACTION100

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