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- EMDB-22169: Molecular structure of the core of amyloid-like fibrils formed by... -

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Basic information

Entry
Database: EMDB / ID: EMD-22169
TitleMolecular structure of the core of amyloid-like fibrils formed by residues 111-214 of FUS
Map data
Sample
  • Complex: FUS low complexity sequence
    • Protein or peptide: RNA-binding protein FUS
KeywordsLow complexity domain / Protein aggregation / Amyloid Fibril / RNA BINDING PROTEIN / PROTEIN FIBRIL
Function / homology
Function and homology information


mRNA stabilization / positive regulation of double-strand break repair via homologous recombination / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / positive regulation of double-strand break repair via homologous recombination / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / 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
RNA-binding protein FUS
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsTycko R / Lee M
CitationJournal: Nat Commun / Year: 2020
Title: Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS.
Authors: Myungwoon Lee / Ujjayini Ghosh / Kent R Thurber / Masato Kato / Robert Tycko /
Abstract: Protein domains without the usual distribution of amino acids, called low complexity (LC) domains, can be prone to self-assembly into amyloid-like fibrils. Self-assembly of LC domains that are nearly ...Protein domains without the usual distribution of amino acids, called low complexity (LC) domains, can be prone to self-assembly into amyloid-like fibrils. Self-assembly of LC domains that are nearly devoid of hydrophobic residues, such as the 214-residue LC domain of the RNA-binding protein FUS, is particularly intriguing from the biophysical perspective and is biomedically relevant due to its occurrence within neurons in amyotrophic lateral sclerosis, frontotemporal dementia, and other neurodegenerative diseases. We report a high-resolution molecular structural model for fibrils formed by the C-terminal half of the FUS LC domain (FUS-LC-C, residues 111-214), based on a density map with 2.62 Å resolution from cryo-electron microscopy (cryo-EM). In the FUS-LC-C fibril core, residues 112-150 adopt U-shaped conformations and form two subunits with in-register, parallel cross-β structures, arranged with quasi-2 symmetry. All-atom molecular dynamics simulations indicate that the FUS-LC-C fibril core is stabilized by a plethora of hydrogen bonds involving sidechains of Gln, Asn, Ser, and Tyr residues, both along and transverse to the fibril growth direction, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions. Nuclear magnetic resonance measurements additionally show that portions of disordered residues 151-214 remain highly dynamic in FUS-LC-C fibrils and that fibrils formed by the N-terminal half of the FUS LC domain (FUS-LC-N, residues 2-108) have the same core structure as fibrils formed by the full-length LC domain. These results contribute to our understanding of the molecular structural basis for amyloid formation by FUS and by LC domains in general.
History
DepositionJun 15, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xfm
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xfm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22169.png

Downloads & links

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Map

FileDownload / File: emd_22169.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.10251353 - 0.19740163
Average (Standard dev.)0.00006598027 (±0.0028924437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z429.600429.600429.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1030.1970.000

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Supplemental data

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Sample components

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Entire : FUS low complexity sequence

EntireName: FUS low complexity sequence
Components
  • Complex: FUS low complexity sequence
    • Protein or peptide: RNA-binding protein FUS

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Supramolecule #1: FUS low complexity sequence

SupramoleculeName: FUS low complexity sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: C-terminal domain of FUS low complexity domain (111-214)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.4 kDa/nm

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Macromolecule #1: RNA-binding protein FUS

MacromoleculeName: RNA-binding protein FUS / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.024784 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSYGSSSQSS SYGQPQSGSY SQQPSYGGQQ QSYGQQQSYN PPQGYGQQNQ YNSSSGGGGG GGGGGNYGQD QSSMSSGGGS GGGYGNQDQ SGGGGSGGYG QGDRG

UniProtKB: RNA-binding protein FUS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris HCl / Details: 20 mM 2-mercaptoethanol, 0.1 mM PMSF
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Pressure: 0.039 kPa
Details: The grid was glow discharged immediately before use.
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 93 K / Instrument: LEICA PLUNGER
Details: Preblot for 10 seconds and blot for 5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3800 pixel / Digitization - Dimensions - Height: 3700 pixel / Number grids imaged: 2 / Number real images: 2404 / Average exposure time: 6.0 sec. / Average electron dose: 47.0 e/Å2
Details: 58185 fibril segments were manually selected from 2404 micrographs
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 499206
Details: 499206 of particles were extracted from the 58185 fibril segments using a 400-pixel box size and 91.6% overlap.
Startup modelType of model: NONE / Details: featureless cylinder
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Details: 4.8-Angstrom helical rise and -2.0 degree helical twist
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
Details: The major class which contains 69% of the particles was selected for further refinement
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: 3D refinement and post-processing were performed with 21 (screw) symmetry
Number images used: 275520
DetailsGatan Imaging Filter (GIF) Quantum LS

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Atomic model buiding 1

DetailsManually generated model was fit into the density using PHENIX and UCSF Chimera. Further refinements were performed using Xplor-NIH.
RefinementProtocol: OTHER
Output model

PDB-6xfm:
Molecular structure of the core of amyloid-like fibrils formed by residues 111-214 of FUS

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