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- EMDB-8857: MicroED structure of the segment, NFGEFS, from the A315E familial... -

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Basic information

Entry
Database: EMDB / ID: EMD-8857
TitleMicroED structure of the segment, NFGEFS, from the A315E familial variant of the low complexity domain of TDP-43, residues 312-317
Map dataNFGEFS from the A315E familial variant of the low complexity domain of TDP-43, residues 312-317
Sample
  • Organelle or cellular component: Segment from TDP-43
    • Protein or peptide: TAR DNA-binding protein 43
  • Ligand: water
KeywordsAmyloid / LARKS / TDP-43 / PROTEIN FIBRIL
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 / Resolution: 1.0 Å
AuthorsGuenther EL / Sawaya MR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)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
DepositionJul 24, 2017-
Header (metadata) releaseAug 30, 2017-
Map releaseMay 23, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wkb
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8857.png

Downloads & links

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Map

FileDownload / File: emd_8857.map.gz / Format: CCP4 / Size: 116.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNFGEFS from the A315E familial variant of the low complexity domain of TDP-43, residues 312-317
Voxel sizeX: 0.32402 Å / Y: 0.335 Å / Z: 0.30625 Å
Density
Contour LevelBy AUTHOR: 0.41 / Movie #1: 0.41
Minimum - Maximum-0.5714499 - 2.15831
Average (Standard dev.)-0.000000000235118 (±0.26856422)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions1321614
Spacing1325216
CellA: 42.77064 Å / B: 17.42 Å / C: 4.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.324022727272730.3350.30625
M x/y/z1325216
origin x/y/z0.0000.0000.000
length x/y/z42.77117.4204.900
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ1321416
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS1613214
D min/max/mean-0.5712.158-0.000

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Supplemental data

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Sample components

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Entire : Segment from TDP-43

EntireName: Segment from TDP-43
Components
  • Organelle or cellular component: Segment from TDP-43
    • Protein or peptide: TAR DNA-binding protein 43
  • Ligand: water

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Supramolecule #1: Segment from TDP-43

SupramoleculeName: Segment from TDP-43 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 699.709 Da
SequenceString:
NFGEFS

UniProtKB: TAR DNA-binding protein 43

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Macromolecule #2: water

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

ChemComp-HOH:
WATER / 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: 7.5 / Component - Name: 1x PBS / Details: 1x PBS, pH 7.5
VitrificationCryogen name: ETHANE

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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: 1840 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Average electron dose: 3.4 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Crystallography statisticsNumber intensities measured: 18942 / Number structure factors: 2032 / Fourier space coverage: 88.7 / R sym: 28.3 / R merge: 28.3 / Overall phase error: 0.001 / Overall phase residual: 0.001 / Phase error rejection criteria: 1 / High resolution: 1.0 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.0 Å / Shell - Low resolution: 1.03 Å / Shell - Number structure factors: 110 / Shell - Phase residual: 0.001 / Shell - Fourier space coverage: 78 / Shell - Multiplicity: 4.8
Molecular replacementSoftware - Name: SHELXD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Merging software listSoftware - Name: XSCALE

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