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- PDB-6cvj: Model of synthetic tau (four tandem repeats of first repeat seque... -

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Basic information

Entry
Database: PDB / ID: 6cvj
TitleModel of synthetic tau (four tandem repeats of first repeat sequence) bound to the microtubule
Components
  • Microtubule-associated protein tauTau protein
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / microtubule / tau
Function / homologyTubulin/FtsZ, 2-layer sandwich domain / Beta tubulin, autoregulation binding site / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Resolution of Sister Chromatid Cohesion / Tubulin/FtsZ, C-terminal domain superfamily / Separation of Sister Chromatids / Tubulin, conserved site / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane ...Tubulin/FtsZ, 2-layer sandwich domain / Beta tubulin, autoregulation binding site / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Resolution of Sister Chromatid Cohesion / Tubulin/FtsZ, C-terminal domain superfamily / Separation of Sister Chromatids / Tubulin, conserved site / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Activation of AMPK downstream of NMDARs / Recruitment of mitotic centrosome proteins and complexes / Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP proteins tubulin-binding repeat signature. / Microtubule-associated protein Tau / Tubulin-beta mRNA autoregulation signal. / Tubulin subunits alpha, beta, and gamma signature. / Tubulin C-terminal domain / Tubulin/FtsZ, C-terminal / Tau and MAP protein, tubulin-binding repeat / Tubulin/FtsZ, GTPase domain superfamily / Tubulin / Tubulin/FtsZ family, GTPase domain / Loss of proteins required for interphase microtubule organization from the centrosome / Kinesins / Tubulin, C-terminal / Carboxyterminal post-translational modifications of tubulin / Beta tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Alpha tubulin / COPI-mediated anterograde transport / RHO GTPases Activate Formins / RHO GTPases activate IQGAPs / Intraflagellar transport / Anchoring of the basal body to the plasma membrane / Cilium Assembly / Hedgehog 'off' state / Recycling pathway of L1 / Recruitment of NuMA to mitotic centrosomes / Microtubule associated protein, tubulin-binding repeat / Tubulin/FtsZ, GTPase domain / plus-end-directed organelle transport along microtubule / positive regulation of diacylglycerol kinase activity / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / regulation of chromosome organization / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / rRNA metabolic process / tubulin complex / microtubule lateral binding / generation of neurons / negative regulation of mitochondrial fission / regulation of long-term synaptic depression / negative regulation of mitochondrial membrane potential / microtubule polymerization / lipoprotein particle binding / axonal transport of mitochondrion / intracellular distribution of mitochondria / axon development / positive regulation of cellular protein localization / negative regulation of tubulin deacetylation / AT DNA binding / regulation of mitochondrial fission / glial cell projection / central nervous system neuron development / regulation of calcium-mediated signaling / negative regulation of kinase activity / somatodendritic compartment / internal protein amino acid acetylation / regulation of microtubule polymerization / dynactin binding / stress granule assembly / receptor ligand activity / cellular response to brain-derived neurotrophic factor stimulus / axolemma / supramolecular fiber organization / cytoplasmic microtubule organization / main axon / regulation of microtubule polymerization or depolymerization / regulation of response to DNA damage stimulus / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / apolipoprotein binding / positive regulation of microtubule polymerization / axon cytoplasm / synapse assembly / phosphatidylinositol binding / microtubule-based process / amyloid fibril formation / microglial cell activation / nuclear periphery
Function and homology information
Specimen sourceHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.2 Å resolution
AuthorsNogales, E. / Kellogg, E.H.
Funding supportUnited States , 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences051487United States
CitationJournal: Science / Year: 2018
Title: Near-atomic model of microtubule-tau interactions.
Authors: Elizabeth H Kellogg / Nisreen M A Hejab / Simon Poepsel / Kenneth H Downing / Frank DiMaio / Eva Nogales /
Abstract: Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into ...Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into fibrils implicated in Alzheimer's disease. It is unclear which tau residues are crucial for tau-MT interactions, where tau binds on MTs, and how it stabilizes them. We used cryo-electron microscopy to visualize different tau constructs on MTs and computational approaches to generate atomic models of tau-tubulin interactions. The conserved tubulin-binding repeats within tau adopt similar extended structures along the crest of the protofilament, stabilizing the interface between tubulin dimers. Our structures explain the effect of phosphorylation on MT affinity and lead to a model of tau repeats binding in tandem along protofilaments, tethering together tubulin dimers and stabilizing polymerization interfaces.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 28, 2018 / Release: May 23, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 23, 2018Structure modelrepositoryInitial release
1.1Jun 27, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Jan 16, 2019Structure modelData collection / Database referencescitation_author_citation_author.identifier_ORCID

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin beta chain
D: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3578
Polyers171,9234
Non-polymers1,4344
Water0
1
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin beta chain
D: Microtubule-associated protein tau
hetero molecules
x 30


Theoretical massNumber of molelcules
Total (without water)5,200,712240
Polyers5,157,696120
Non-polymers43,017120
Water0
TypeNameSymmetry operationNumber
helical symmetry operation30
2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 30 / Rise per n subunits: 8.65 Å / Rotation per n subunits: -25.75 deg.

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Components

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Protein/peptide , 3 types, 4 molecules ABCD

#1: Protein/peptide Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein/peptide Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein/peptide Microtubule-associated protein tau / Tau protein


Mass: 21903.201 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10636*PLUS

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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 2 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Ternary complex of alpha-beta tubulin with synthetic (R1x4) tauCOMPLEX1,2,30MULTIPLE SOURCES
2Tubulin alpha-1B chainCOMPLEX11NATURAL
3Tubulin beta chainCOMPLEX21NATURAL
4Microtubule-associated protein tauCOMPLEX31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129823Sus scrofa (pig)
239823Sus scrofa (pig)
349606Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer ID
180 mMPIPESC8H18N2O6S21
21 mMEGTAC14H24N2O101
31 mMMagnesium ChlorideMgCl21
41 mMDTTC4H10O2S21
51 mMGuanine tri-phosphateGTP1
SpecimenConc.: 0.5 mg/ml
Details: tubulin concentration is 0.5 mg/mL, tau concentration is 1 mg/mL
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 310.15 kelvins
Details: blot force 10 pN, 6 second blot time. used C-flat 1.2/1.3 holey grids. First 2 uL of microtubules were adhered to grid for 30 seconds, followed by 2 4 uL washes of tau with 30 second incubation for each wash

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 35714 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.5 sec. / Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 712
EM imaging opticsPhase plate: none
Image scansMovie frames/image: 30

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Processing

EM software
IDNameVersionCategory
1Appionparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Rosettamodel fitting
9EMAN2initial Euler assignment
10FREALIGN9.09final Euler assignment
12FREALIGN9.093D reconstruction
Image processingDetails: used motioncorr2 to correct for beam-induced motion
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -25.75 deg. / Axial rise/subunit: 8.65 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 57526
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 40522 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingOverall b value: 120 / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: real space correlation

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