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- EMDB-7467: SWGMMGMLASQ segment from the low complexity domain of TDP-43 -

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Basic information

Entry
Database: EMDB / ID: EMD-7467
TitleSWGMMGMLASQ segment from the low complexity domain of TDP-43
Map dataSWGMMGMLASQ segment from the low complexity domain of TDP-43, residues 333-343
Sample
  • Complex: crystal of SWGMMGMLASQ
    • Protein or peptide: TAR DNA-binding protein 43
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 / molecular condensate scaffold activity / response to endoplasmic reticulum stress ...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 / molecular condensate scaffold activity / response to endoplasmic reticulum stress / RNA splicing / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / positive regulation of insulin secretion / mRNA processing / cytoplasmic stress granule / positive regulation of protein import into nucleus / rhythmic process / double-stranded DNA binding / regulation of gene expression / 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 / Rodriguez JA / 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 15, 2018-
Header (metadata) releaseMar 7, 2018-
Map releaseMay 23, 2018-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cfh
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7467.png

Downloads & links

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Map

FileDownload / File: emd_7467.map.gz / Format: CCP4 / Size: 216.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSWGMMGMLASQ segment from the low complexity domain of TDP-43, residues 333-343
Voxel sizeX: 0.35667 Å / Y: 0.4 Å / Z: 0.41635 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 0.15
Minimum - Maximum-0.62345374 - 1.1086956
Average (Standard dev.)1.7381664e-10 (±0.20651858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions242496
Spacing242496
CellA: 8.56008 Å / B: 9.6 Å / C: 39.9696 Å
α: 97.17 ° / β: 92.89 ° / γ: 105.94 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.356666666666670.40.41635416666667
M x/y/z242496
origin x/y/z0.0000.0000.000
length x/y/z8.5609.60039.970
α/β/γ97.17092.890105.940
start NX/NY/NZ000
NX/NY/NZ242496
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS242496
D min/max/mean-0.6231.1090.000

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Supplemental data

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Sample components

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Entire : crystal of SWGMMGMLASQ

EntireName: crystal of SWGMMGMLASQ
Components
  • Complex: crystal of SWGMMGMLASQ
    • Protein or peptide: TAR DNA-binding protein 43

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Supramolecule #1: crystal of SWGMMGMLASQ

SupramoleculeName: crystal of SWGMMGMLASQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TAR DNA-binding protein 43

MacromoleculeName: TAR DNA-binding protein 43 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.198436 KDa
SequenceString:
SWGMMGMLAS Q

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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

Concentration24 mg/mL
BufferpH: 7.5
Component: (Name: sodium chloride, potassium chloride, dibasic sodium phosphate, monobasic potassium phosphate)
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
Detailscrystal
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 80 hours.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1850 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
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 real images: 891 / Number diffraction images: 100 / Average exposure time: 2.0 sec. / Average electron dose: 0.01 e/Å2
Details: The detector was operated in rolling shutter mode with 2X2 pixel binning.
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Crystal parametersUnit cell - A: 8.56 Å / Unit cell - B: 9.60 Å / Unit cell - C: 39.97 Å / Unit cell - γ: 105.943 ° / Unit cell - α: 97.171 ° / Unit cell - β: 92.895 ° / Space group: P 1
Crystallography statisticsNumber intensities measured: 7695 / Number structure factors: 1819 / Fourier space coverage: 93.5 / R sym: 20.8 / R merge: 20.8 / Overall phase error: 55.72 / Overall phase residual: 55.72 / Phase error rejection criteria: 0 / High resolution: 1.5 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.5 Å / Shell - Low resolution: 13.1675 Å / Shell - Number structure factors: 1819 / Shell - Phase residual: 55.72 / Shell - Fourier space coverage: 93.5 / Shell - Multiplicity: 4.2
Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
Details: Density map was obtained using measured diffraction intensities and phases acquired from a molecular replacement program, phaser.

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 17.4 / Target criteria: maximum likihood
Output model

PDB-6cfh:
SWGMMGMLASQ segment from the low complexity domain of TDP-43

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