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- PDB-8g54: Temperature-dependent structures of tau aggregates -

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Basic information

Entry
Database: PDB / ID: 8g54
TitleTemperature-dependent structures of tau aggregates
ComponentsMicrotubule-associated protein tau
KeywordsPROTEIN FIBRIL / tau / amyloid fibril
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / positive regulation of protein localization to synapse / neurofibrillary tangle / microtubule lateral binding / axonal transport / main axon / phosphatidylinositol bisphosphate binding / tubulin complex ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / positive regulation of protein localization to synapse / neurofibrillary tangle / microtubule lateral binding / axonal transport / main axon / phosphatidylinositol bisphosphate binding / tubulin complex / regulation of long-term synaptic depression / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / intracellular distribution of mitochondria / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / negative regulation of mitochondrial membrane potential / glial cell projection / apolipoprotein binding / axolemma / protein polymerization / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / neurofibrillary tangle assembly / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cytoplasmic microtubule organization / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of protein localization / axon cytoplasm / regulation of calcium-mediated signaling / supramolecular fiber organization / somatodendritic compartment / stress granule assembly / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of microtubule polymerization / phosphatidylinositol binding / nuclear periphery / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / cellular response to reactive oxygen species / astrocyte activation / Hsp90 protein binding / microglial cell activation / synapse organization / cellular response to nerve growth factor stimulus / response to lead ion / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / microtubule cytoskeleton / cell-cell signaling / single-stranded DNA binding / actin binding / protein-folding chaperone binding / cell body / cellular response to heat / growth cone / double-stranded DNA binding / microtubule binding / protein-macromolecule adaptor activity / microtubule / sequence-specific DNA binding / dendritic spine / amyloid fibril formation / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / 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 speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsEl Mammeri, N. / Duan, P. / Dregni, A.J. / Hong, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG059661 United States
CitationJournal: Sci Adv / Year: 2023
Title: Amyloid fibril structures of tau: Conformational plasticity of the second microtubule-binding repeat.
Authors: El Mammeri, N. / Duan, P. / Dregni, A.J. / Hong, M.
History
DepositionFeb 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein tau
B: Microtubule-associated protein tau
C: Microtubule-associated protein tau
D: Microtubule-associated protein tau
E: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)107,2585
Polymers107,2585
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17390 Å2
ΔGint-48 kcal/mol
Surface area12060 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein
Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 21451.641 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPT, MAPTL, MTBT1, TAU / Production host: Escherichia coli (E. coli) / References: UniProt: P10636

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D CC
121anisotropic12D NCA
131anisotropic13D CCC
141anisotropic13D NCACX
151anisotropic12D NCOCX

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Sample preparation

DetailsType: fibrous protein / Details: amyloid fibrils / Label: 15N_13C_sample / Solvent system: 100% H2O
SampleConc.: 5 uM / Component: Microtubule-associated protein tau / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 135 mM / Label: solid sample / pH: 7.4 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5CCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinBruker Biospindata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospinpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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