EMDB-10512: Cryo-EM reconstruction of TypeI tau filaments extracted from the ...

Basic information

• Entry: Database: EMDB / ID: EMD-10512
• Title: Cryo-EM reconstruction of TypeI tau filaments extracted from the brains of an individual (Case 1) with Corticobasal degeneration
• Map data: Cryo-EM reconstruction of TypeI tau filaments extracted from the brains of an individual (Case 1) with Corticobasal degeneration

Sample

• Complex: Tau filaments extracted from the Frontal cortex of a patient with corticobasal degeneration.
  • Protein or peptide: Microtubule-associated protein tauTau protein

Function / homology

Function:

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 / lipoprotein particle binding / 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 / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / 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 / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / regulation of cellular response to heat / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / 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 / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / SH3 domain binding / cellular response to reactive oxygen species / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding

Domain/homology:

: / 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.

Component:

Microtubule-associated protein tau

• Biological species: Homo sapiens (human) / Human (human)
• Method: helical reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Zhang W / Murzin AG / Falcon B / Shi Y / Goedert M / Scheres SHW

Funding support

United Kingdom, 2 items

Organization	Grant number	Country
Medical Research Council (United Kingdom)	MC_UP_A025_1013	United Kingdom
Medical Research Council (United Kingdom)	MC_U105184291	United Kingdom

• Citation: Journal: Nature / Year: 2020; Title: Novel tau filament fold in corticobasal degeneration.; Authors: Wenjuan Zhang / Airi Tarutani / Kathy L Newell / Alexey G Murzin / Tomoyasu Matsubara / Benjamin Falcon / Ruben Vidal / Holly J Garringer / Yang Shi / Takeshi Ikeuchi / Shigeo Murayama / Bernardino Ghetti / Masato Hasegawa / Michel Goedert / Sjors H W Scheres / ; Abstract: Corticobasal degeneration (CBD) is a neurodegenerative tauopathy-a class of disorders in which the tau protein forms insoluble inclusions in the brain-that is characterized by motor and cognitive disturbances. The H1 haplotype of MAPT (the tau gene) is present in cases of CBD at a higher frequency than in controls, and genome-wide association studies have identified additional risk factors. By histology, astrocytic plaques are diagnostic of CBD; by SDS-PAGE, so too are detergent-insoluble, 37 kDa fragments of tau. Like progressive supranuclear palsy, globular glial tauopathy and argyrophilic grain disease, CBD is characterized by abundant filamentous tau inclusions that are made of isoforms with four microtubule-binding repeats. This distinguishes such '4R' tauopathies from Pick's disease (the filaments of which are made of three-repeat (3R) tau isoforms) and from Alzheimer's disease and chronic traumatic encephalopathy (CTE) (in which both 3R and 4R isoforms are found in the filaments). Here we use cryo-electron microscopy to analyse the structures of tau filaments extracted from the brains of three individuals with CBD. These filaments were identical between cases, but distinct from those seen in Alzheimer's disease, Pick's disease and CTE. The core of a CBD filament comprises residues lysine 274 to glutamate 380 of tau, spanning the last residue of the R1 repeat, the whole of the R2, R3 and R4 repeats, and 12 amino acids after R4. The core adopts a previously unseen four-layered fold, which encloses a large nonproteinaceous density. This density is surrounded by the side chains of lysine residues 290 and 294 from R2 and lysine 370 from the sequence after R4.

History

Deposition	Nov 26, 2019	-
Header (metadata) release	Feb 5, 2020	-
Map release	Feb 5, 2020	-
Update	Dec 2, 2020	-
Current status	Dec 2, 2020	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_10512.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Cryo-EM reconstruction of TypeI tau filaments extracted from the brains of an individual (Case 1) with Corticobasal degeneration
• Voxel size: X=Y=Z: 1.15 Å

Density

Contour Level	By AUTHOR: 0.0115 / Movie #1: 0.02
Minimum - Maximum	-0.043497514 - 0.090144835
Average (Standard dev.)	0.00044618914 (±0.003450466)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 330 330 330 Spacing 330 330 330
Cell	A=B=C: 379.5 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.15	1.15	1.15
M x/y/z	330	330	330
origin x/y/z	0.000	0.000	0.000
length x/y/z	379.500	379.500	379.500
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	330	330	330
D min/max/mean	-0.043	0.090	0.000

Supplemental data

Mask #1

• File: emd_10512_msk_1.map

Half map: Half map 1

• File: emd_10512_half_map_1.map
• Annotation: Half map 1

Half map: Half map 2

• File: emd_10512_half_map_2.map
• Annotation: Half map 2

Sample components

Entire : Tau filaments extracted from the Frontal cortex of a patient with...

• Entire: Name: Tau filaments extracted from the Frontal cortex of a patient with corticobasal degeneration.

Components

• Complex: Tau filaments extracted from the Frontal cortex of a patient with corticobasal degeneration.
  • Protein or peptide: Microtubule-associated protein tauTau protein

Supramolecule #1: Tau filaments extracted from the Frontal cortex of a patient with...

• Supramolecule: Name: Tau filaments extracted from the Frontal cortex of a patient with corticobasal degeneration.; type: complex / ID: 1 / Parent: 0 / Macromolecule list: all; Details: Corticobasal degeneration (CBD) is characterised by abundant filamentous tau inclusions that are made of isoforms with four microtubule-binding repeats (4R).
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 460 KDa

Macromolecule #1: Microtubule-associated protein tau

• Macromolecule: Name: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Human (human)
• Molecular weight: Theoretical: 45.919871 KDa

Sequence

String:

MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKSTP TAEDVTAPLV DEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA GHVTQARMVS KSKDGTGSDD KKAKGADGKT KIATPRGAAP P GQKGQANA TRIPAKTPPA PKTPPSSGEP PKSGDRSGYS SPGSPGTPGS RSRTPSLPTP PTREPKKVAV VRTPPKSPSS AK SRLQTAP VPMPDLKNVK SKIGSTENLK HQPGGGKVQI INKKLDLSNV QSKCGSKDNI KHVPGGGSVQ IVYKPVDLSK VTS KCGSLG NIHHKPGGGQ VEVKSEKLDF KDRVQSKIGS LDNITHVPGG GNKKIETHKL TFRENAKAKT DHGAEIVYKS PVVS GDTSP RHLSNVSSTG SIDMVDSPQL ATLADEVSAS LAKQGL

Experimental details

Structure determination

• Method: cryo EM
• Processing: helical reconstruction
• Aggregation state: filament

Sample preparation

• Concentration: 2.0 mg/mL

Buffer

pH: 7.4
Component:

Concentration	Formula	Name
0.02 mol/L	Tris	tris(hydroxymethyl)aminomethane
0.1 mol/L	NaClSodium chloride	sodium chloride

Details: 20 mM Tris, pH 7.4, 100mM NaCl

• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force: -12 ; Blot time: 4s.
• Details: The tau filaments were extracted from the Frontal cortex of a patient with corticobasal degeneration by using sarkosyl and ultracentrifuge.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 1.7 µm
• Specialist optics: Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2567 / Average exposure time: 10.0 sec. / Average electron dose: 1.346 e/Ų; Details: Images were collected in movie-mode at 40 frames every 10 seconds
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Segment selection: Number selected: 135646 / Software - Name: RELION (ver. 3.0) / Details: Manually picked
• CTF correction: Software - Name: CTFFIND (ver. 4.1); Details: Aligned, non-dose-weighted micrographs were used to estimate the contrast transfer function (CTF) using CTFFIND4.1
• Startup model: Type of model: OTHER; Details: An initial 3D reference was reconstructed from the 2D class averages de novo.
• Final angle assignment: Type: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
• Final reconstruction: Number classes used: 3 ; Applied symmetry - Helical parameters - Δz: 4.786 Å; Applied symmetry - Helical parameters - Δ&Phi: -0.845 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 24073
• Details: Movie frames were gain-corrected, aligned, dose weighted and then summed into a single micrograph using MOTIONCOR2 (Zheng et al., 2017)

Atomic model buiding 1

• Details: A stack of three consecutive monomers was refined to preserve nearest-neighbour interactions for the middle chain. Because most residues adopted cross strand conformation, hydrogen-bond restraints were imposed to preserve a parallel, in-register hydrogen bonding pattern in earlier stages of Fourier-space refinements. Local symmetry restraints were imposed to keep all beta strand rungs identical. 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.
• Refinement: Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 26.63 / Target criteria: Fourier shell correlation

Output model

PDB-6tjo:
Cryo-EM structure of TypeI tau filaments extracted from the brains of individuals with Corticobasal degeneration