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- EMDB-7466: Segment NFGTFS, with familial mutation A315T and phosphorylated t... -

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Basic information

Entry
Database: EMDB / ID: EMD-7466
TitleSegment NFGTFS, with familial mutation A315T and phosphorylated threonine, from the low complexity domain of TDP-43, residues 312-317
Map data
Sample
  • Complex: crystal of NFGTFS phosphorylated on threonine.
    • Protein or peptide: NFGTFS
  • Ligand: water
Function / homology
Function and homology information


nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing / negative regulation of protein phosphorylation / molecular condensate scaffold activity / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / positive regulation of insulin secretion / mRNA processing / positive regulation of protein import into nucleus / cytoplasmic stress granule / rhythmic process / regulation of gene expression / double-stranded DNA binding / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM
AuthorsGuenther EL / Cao Q / Boyer DR / Sawaya MR / Eisenberg DS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG029430 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.
Authors: Elizabeth L Guenther / Qin Cao / Hamilton Trinh / Jiahui Lu / Michael R Sawaya / Duilio Cascio / David R Boyer / Jose A Rodriguez / Michael P Hughes / David S Eisenberg /
Abstract: The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is ...The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation.
History
DepositionFeb 13, 2018-
Header (metadata) releaseMar 7, 2018-
Map releaseMay 23, 2018-
UpdateJun 30, 2021-
Current statusJun 30, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cf4
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7466.png

Downloads & links

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Map

FileDownload / File: emd_7466.map.gz / Format: CCP4 / Size: 525.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.2 Å/pix.
x 7 pix.
= 4.728 Å		0.2 Å/pix.
x 120 pix.
= 23.64 Å		0.19 Å/pix.
x 160 pix.
= 30.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.197 Å / Y: 0.197 Å / Z: 0.188 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-1.8127885 - 16.370777
Average (Standard dev.)-0.00024257644 (±1.13569)
SymmetrySpace group: 19
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions1201607
Spacing12024160
CellA: 23.64 Å / B: 4.7279997 Å / C: 30.079998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.1970.1970.188
M x/y/z12024160
origin x/y/z0.0000.0000.000
length x/y/z23.6404.72830.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ1207160
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS1601207
D min/max/mean-1.81316.371-0.000

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Supplemental data

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Sample components

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Entire : crystal of NFGTFS phosphorylated on threonine.

EntireName: crystal of NFGTFS phosphorylated on threonine.
Components
  • Complex: crystal of NFGTFS phosphorylated on threonine.
    • Protein or peptide: NFGTFS
  • Ligand: water

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Supramolecule #1: crystal of NFGTFS phosphorylated on threonine.

SupramoleculeName: crystal of NFGTFS phosphorylated on threonine. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NFGTFS

MacromoleculeName: NFGTFS / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 751.679 Da
SequenceString:
NFG(TPO)FS

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Crystal formationLipid mixture: none / Instrument: microcentrifuge tube / Atmosphere: air, sealed chamber / Temperature: 310.0 K / Time: 4.0 DAY
Details: Crystals were prepared by shaking peptide in microcentrifuge tube at 37 deg Celsius for 4 days.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 100.0 K / Max: 100.0 K
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number diffraction images: 100 / Average exposure time: 3.0 sec. / Average electron dose: 0.01 e/Å2
Details: The detector was operated in rolling shutter mode with 2X2 pixel binning.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 819 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: SHELXD (ver. 2013/2) / Software - details: direct methods
Details: Density map was obtained using measured diffraction intensities and phases acquired from a crystallographic direct methods program, shelxd.
Crystal parametersUnit cell - A: 23.650 Å / Unit cell - B: 4.720 Å / Unit cell - C: 30.060 Å / Unit cell - γ: 90.00 ° / Unit cell - α: 90.00 ° / Unit cell - β: 90.00 ° / Space group: P 21 21 21
Crystallography statisticsNumber intensities measured: 15891 / Number structure factors: 4177 / Fourier space coverage: 86.6 / R sym: 17.2 / R merge: 17.2 / Overall phase error: 32.2 / Overall phase residual: 32.2 / Phase error rejection criteria: 0 / High resolution: 0.75 Å
Shell:
Shell IDHigh resolutionLow resolutionNumber structure factorsPhase residualFourier space coverageMultiplicity
17.65 Å1.08 Å130020.9685.03.6
21.08 Å0.86 Å124137.0388.03.9
30.86 Å0.75 Å120939.3888.03.9

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 19.6 / Target criteria: maximum likihood
Output model

PDB-6cf4:
Segment NFGTFS, with familial mutation A315T and phosphorylated threonine, from the low complexity domain of TDP-43, residues 312-317

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