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- PDB-9g13: VHH H3-2 in complex with Tau C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 9g13
TitleVHH H3-2 in complex with Tau C-terminal peptide
Components
  • Isoform Tau-F of Microtubule-associated protein tau
  • VHH H3-2
KeywordsIMMUNE SYSTEM / VHH / Nanobody / Tau
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / rRNA metabolic process / internal protein amino acid acetylation / regulation of chromosome organization / regulation of mitochondrial fission / axonal transport of mitochondrion / axon development / intracellular distribution of mitochondria / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / apolipoprotein binding / protein polymerization / axolemma / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / regulation of cellular response to heat / cytoplasmic microtubule organization / stress granule assembly / supramolecular fiber organization / regulation of calcium-mediated signaling / axon cytoplasm / somatodendritic compartment / positive regulation of microtubule polymerization / 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 / microglial cell activation / synapse organization / Hsp90 protein binding / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / memory / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton organization / SH3 domain binding / cellular response to reactive oxygen species / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-folding chaperone binding / protein-macromolecule adaptor activity / single-stranded DNA binding / actin binding / cellular response to heat / cell body / 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 / dendrite / 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 speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDupre, E. / Landrieu, I. / Danis, C. / Hanoulle, X. / Mortelecque, J.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE44-0016 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-01 France
CitationJournal: To Be Published
Title: VHH H3-2 in complex with Tau C-terminal peptide
Authors: Dupre, E. / Landrieu, I. / Danis, C. / Hanoulle, X. / Mortelecque, J.
History
DepositionJul 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VHH H3-2
B: Isoform Tau-F of Microtubule-associated protein tau
E: VHH H3-2
F: Isoform Tau-F of Microtubule-associated protein tau
C: VHH H3-2
D: Isoform Tau-F of Microtubule-associated protein tau
G: VHH H3-2
H: Isoform Tau-F of Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)63,6788
Polymers63,6788
Non-polymers00
Water8,467470
1
A: VHH H3-2
B: Isoform Tau-F of Microtubule-associated protein tau
C: VHH H3-2
D: Isoform Tau-F of Microtubule-associated protein tau


  • defined by author&software
  • Evidence: gel filtration
  • 31.8 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)31,8394
Polymers31,8394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-49 kcal/mol
Surface area14020 Å2
MethodPISA
2
E: VHH H3-2
F: Isoform Tau-F of Microtubule-associated protein tau
G: VHH H3-2
H: Isoform Tau-F of Microtubule-associated protein tau


  • defined by author&software
  • Evidence: gel filtration
  • 31.8 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)31,8394
Polymers31,8394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-46 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.394, 76.346, 95.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
VHH H3-2


Mass: 14270.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide
Isoform Tau-F of Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1648.923 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.02 Å3/Da / Density % sol: 39.09 % / Description: Hexagonal pillars
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 23% PEG-MME 2000, 0.1 M potassium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564977646 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564977646 Å / Relative weight: 1
ReflectionResolution: 1.8→45.549 Å / Num. obs: 48459 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Net I/σ(I): 19.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-45.519.30.0374520.9920.0170.041
1.8-1.8410.72.58628130.7211.1782.846

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Cootmodel building
Aimlessdata scaling
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.549 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.04 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2312 2348 4.851 %
Rwork0.1717 46050 -
all0.174 --
obs-48398 99.944 %
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: 35.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.396 Å20 Å2-0 Å2
2---0.395 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 0 470 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163912
X-RAY DIFFRACTIONr_angle_refined_deg2.3761.8035873
X-RAY DIFFRACTIONr_angle_other_deg0.8241.7488974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.826529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82810686
X-RAY DIFFRACTIONr_dihedral_angle_6_deg1410190
X-RAY DIFFRACTIONr_chiral_restr0.1230.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021104
X-RAY DIFFRACTIONr_nbd_refined0.2250.2674
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.23473
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22009
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.22403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2340
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1920.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.236
X-RAY DIFFRACTIONr_nbd_other0.2010.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2570.232
X-RAY DIFFRACTIONr_mcbond_it5.9323.742200
X-RAY DIFFRACTIONr_mcbond_other5.913.7412200
X-RAY DIFFRACTIONr_mcangle_it8.5676.6652737
X-RAY DIFFRACTIONr_mcangle_other8.5666.6672738
X-RAY DIFFRACTIONr_scbond_it6.5944.0442141
X-RAY DIFFRACTIONr_scbond_other6.5874.0432140
X-RAY DIFFRACTIONr_scangle_it9.3437.183134
X-RAY DIFFRACTIONr_scangle_other9.3417.1813135
X-RAY DIFFRACTIONr_lrange_it12.28349.5024831
X-RAY DIFFRACTIONr_lrange_other12.30547.3954720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3261760.25633410.25935220.9420.96899.8580.242
1.847-1.8970.3031640.24232600.24534240.9490.9691000.223
1.897-1.9520.2591670.20732000.2133720.9580.97599.85170.186
1.952-2.0120.281880.18730540.19232430.9520.97799.96920.169
2.012-2.0780.2531620.18230230.18531860.960.97899.96860.167
2.078-2.1510.2441470.18128670.18430140.9620.9791000.168
2.151-2.2320.2481380.17428180.17729560.960.9811000.162
2.232-2.3230.2711480.18127060.18628550.9540.97999.9650.169
2.323-2.4260.211190.16526240.16727430.9720.9831000.157
2.426-2.5440.2521160.17725200.1826360.960.981000.169
2.544-2.6810.261100.17523620.17924720.9560.981000.17
2.681-2.8430.2211330.17122360.17323690.9690.9811000.17
2.843-3.0380.1861050.15321350.15522420.9780.98699.91080.155
3.038-3.280.255790.18320100.18620890.960.9811000.192
3.28-3.5920.207820.16818370.1719190.9730.9861000.181
3.592-4.0120.206750.15916930.16117680.9710.9851000.179
4.012-4.6270.181750.12514750.12715500.9820.991000.147
4.627-5.6530.197730.14412790.14613520.9820.991000.175
5.653-7.9330.249650.2129980.21410630.9690.9791000.243
7.933-45.5490.308260.2096120.2136460.9080.96998.76160.263

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