[English] 日本語
Yorodumi
- PDB-6qjm: Cryo-EM structure of heparin-induced 2N4R tau twister filaments -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6qjm
TitleCryo-EM structure of heparin-induced 2N4R tau twister filaments
ComponentsMicrotubule-associated protein tauTau protein
KeywordsPROTEIN FIBRIL / Recombinant tau protein / heparin / filament / cross-beta structure
Function / homologyTau and MAP proteins tubulin-binding repeat signature. / Activation of AMPK downstream of NMDARs / Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP protein, tubulin-binding repeat / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / axonal transport / plus-end-directed organelle transport along microtubule / positive regulation of diacylglycerol kinase activity ...Tau and MAP proteins tubulin-binding repeat signature. / Activation of AMPK downstream of NMDARs / Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP protein, tubulin-binding repeat / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / axonal transport / plus-end-directed organelle transport along microtubule / positive regulation of diacylglycerol kinase activity / neurofibrillary tangle assembly / histone-dependent DNA binding / 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 / lipoprotein particle binding / microtubule polymerization / 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 / central nervous system neuron development / glial cell projection / regulation of calcium-mediated signaling / negative regulation of kinase activity / internal protein amino acid acetylation / somatodendritic compartment / 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 / amyloid fibril formation / microglial cell activation / nuclear periphery / synapse organization / regulation of autophagy / regulation of synaptic plasticity / astrocyte activation / cellular response to nerve growth factor stimulus / cytoplasmic ribonucleoprotein granule / protein phosphatase 2A binding / positive regulation of superoxide anion generation / Hsp90 protein binding / microtubule cytoskeleton organization / protein binding, bridging / memory / cellular response to reactive oxygen species / microtubule cytoskeleton / cell body / regulation of cellular response to heat / neuron projection development / single-stranded DNA binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / response to lead ion / positive regulation of neuron death / SH3 domain binding / learning or memory / growth cone / intracellular / actin binding / cell-cell signaling / cellular response to heat / double-stranded DNA binding / chaperone binding / protein complex oligomerization / microtubule / microtubule binding / protein homooligomerization / dendritic spine / negative regulation of gene expression / nuclear speck / sequence-specific DNA binding / membrane raft / neuron projection
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsZhang, W. / Falcon, B. / Murzin, A.G. / Fan, J. / Crowther, R.A. / Goedert, M. / Scheres, S.H.W.
Funding supportUnited Kingdom , 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1013United Kingdom
Medical Research Council (United Kingdom)MC_U105184291United Kingdom
CitationJournal: Elife / Year: 2019
Title: Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer's and Pick's diseases.
Authors: Wenjuan Zhang / Benjamin Falcon / Alexey G Murzin / Juan Fan / R Anthony Crowther / Michel Goedert / Sjors Hw Scheres
Abstract: Assembly of microtubule-associated protein tau into filamentous inclusions underlies a range of neurodegenerative diseases. Tau filaments adopt different conformations in Alzheimer's and Pick's ...Assembly of microtubule-associated protein tau into filamentous inclusions underlies a range of neurodegenerative diseases. Tau filaments adopt different conformations in Alzheimer's and Pick's diseases. Here, we used cryo- and immuno- electron microscopy to characterise filaments that were assembled from recombinant full-length human tau with four (2N4R) or three (2N3R) microtubule-binding repeats in the presence of heparin. 2N4R tau assembles into multiple types of filaments, and the structures of three types reveal similar 'kinked hairpin' folds, in which the second and third repeats pack against each other. 2N3R tau filaments are structurally homogeneous, and adopt a dimeric core, where the third repeats of two tau molecules pack in a parallel manner. The heparin-induced tau filaments differ from those of Alzheimer's or Pick's disease, which have larger cores with different repeat compositions. Our results illustrate the structural versatility of amyloid filaments, and raise questions about the relevance of in vitro assembly.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 24, 2019 / Release: Feb 27, 2019

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4564
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,5673
Polyers15,5673
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, We used Thioflavin T fluorescence to check the kinetic assays of the filament assembly., microscopy, We used negative-stain electron microscopy to check the morphology of assembled filaments.
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)7080
ΔGint (kcal/M)-19
Surface area (Å2)7620
MethodPISA

-
Components

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


Mass: 5189.081 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPT, MAPTL, MTBT1, TAUTau protein / Plasmid name: pRK172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10636

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: heparin-induced 2N4R tau twister filaments / Type: COMPLEX
Details: Recombinant tau protein was induced into filaments by incubation with heparin at 37 C for 3 days
Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 45.85 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: PRK172
Buffer solutionDetails: 20 mM Tris, pH 7.4, 100mM NaCl / pH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
10.02 mol/Ltris(hydroxymethyl)aminomethaneTris1
20.1 mol/Lsodium chlorideNaCl1
SpecimenConc.: 2 mg/ml
Details: Recombinant tau protein was induced into filaments by incubation with heparin at 37 C for 3 days. The filaments were pronase-treated before making Cryo-grids.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: Blot force: -12 ; Blot time: 4s

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 1700 nm / Cs: 2 mm / C2 aperture diameter: 5 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingAverage exposure time: 1 sec. / Electron dose: 48 e/Å2
Details: Images were collected in movie-mode at 30 frames per second
Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 717
Image scansSampling size: 14 microns / Width: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1RELION3.0particle selection
2EPU1.5.0.1243RELimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.9.1model fitting
9RELION3.0initial Euler assignment
10RELION3.0final Euler assignment
11RELION3.0classification
12RELION3.03D reconstruction
13REFMAC5.8.0236model refinement
14PHENIXdev-2919-000model refinement
Image processingDetails: Movie frames were gain-corrected, aligned, dose weighted and then summed into a single micrograph using MOTIONCOR2 (Zheng et al., 2017)
CTF correctionDetails: Aligned, non-dose-weighted micrographs were used to estimate the contrast transfer function (CTF) using CTFFIND4.1
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.38 deg. / Axial rise/subunit: 4.7 Å / Axial symmetry: C1
Particle selectionDetails: Manually picked / Number of particles selected: 187555
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 141461 / Algorithm: FOURIER SPACE / Details: we performed two rounds of 3D auto-refinement. / Number of class averages: 6 / Symmetry type: HELICAL
Atomic model buildingDetails: A stack of three consecutive monomers was refined to preserve nearest-neighbour interactions for the middle chain. Side-chain clashes were detected using MOLPROBITY, and corrected by iterative cycles of real-space refinement in COOT and Fourier-space refinement in REFMAC and PHENIX. For each refined structure, separate model refinements were performed against a single half-map, and the resulting model was compared to the other half-map to confirm the absence of overfitting.
Overall b value: 58.51 / Ref protocol: AB INITIO MODEL / Ref space: RECIPROCAL / Target criteria: Fourier shell correlation

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more