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- EMDB-8765: MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of T... -

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Basic information

Entry
Database: EMDB / ID: EMD-8765
TitleMicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257
Map dataPeptide DLIIKGISVHI from the RRM2 of TDP-43, residues 247-257
Sample
  • Complex: DLIIKGISVHI fibril
    • Protein or peptide: TAR DNA-binding protein 43
KeywordsAmyloid / steric zipper / 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
AuthorsGuenther EL / Sawaya MR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1616265 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.
Authors: Elizabeth L Guenther / Peng Ge / Hamilton Trinh / Michael R Sawaya / Duilio Cascio / David R Boyer / Tamir Gonen / Z Hong Zhou / David S Eisenberg /
Abstract: Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a ...Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the DLIIKGISVHI segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.
History
DepositionJun 13, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseFeb 21, 2018-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w52
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8765.png

Downloads & links

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Map

FileDownload / File: emd_8765.map.gz / Format: CCP4 / Size: 1.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPeptide DLIIKGISVHI from the RRM2 of TDP-43, residues 247-257
Voxel sizeX: 0.443 Å / Y: 0.338 Å / Z: 0.417 Å
Density
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.22446074 - 0.7162638
Average (Standard dev.)0.0020431273 (±0.11619716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-59-84-19
Dimensions8010152
Spacing5210180
CellA: 23.036 Å / B: 34.138 Å / C: 33.36 Å
α: 80.875 ° / β: 86.373 ° / γ: 89.775 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.4430.3380.417
M x/y/z5210180
origin x/y/z0.0000.0000.000
length x/y/z23.03634.13833.360
α/β/γ80.87586.37389.775
start NX/NY/NZ-59-19-84
NX/NY/NZ8052101
MAP C/R/S312
start NC/NR/NS-84-59-19
NC/NR/NS1018052
D min/max/mean-0.2240.7160.002

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Supplemental data

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Sample components

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Entire : DLIIKGISVHI fibril

EntireName: DLIIKGISVHI fibril
Components
  • Complex: DLIIKGISVHI fibril
    • Protein or peptide: TAR DNA-binding protein 43

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Supramolecule #1: DLIIKGISVHI fibril

SupramoleculeName: DLIIKGISVHI fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: This peptide was synthesized and crystallized.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.03 kDa/nm

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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: 1.209479 KDa
SequenceString:
DLIIKGISVH I

UniProtKB: TAR DNA-binding protein 43

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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: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1840 mm
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 3.4 e/Å2

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Image processing

Crystallography statisticsNumber intensities measured: 9353 / Number structure factors: 1037 / Fourier space coverage: 73.4 / R sym: 20.3 / R merge: 20.3 / Overall phase error: 0.001 / Overall phase residual: 0.001 / Phase error rejection criteria: 1 / High resolution: 1.4 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.4 Å / Shell - Low resolution: 1.48 Å / Shell - Number structure factors: 139 / Shell - Phase residual: 0.001 / Shell - Fourier space coverage: 62.1 / Shell - Multiplicity: 6.71
Molecular replacementSoftware - Name: Phaser
Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
Merging software listSoftware - Name: XSCALE

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