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- EMDB-32092: Cryo-EM structure of amyloid fibril formed by FUS low complexity ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32092
TitleCryo-EM structure of amyloid fibril formed by FUS low complexity domain
Map data
Sample
  • Organelle or cellular component: Amyloid fibril formed by FUS low complexity domain
    • Protein or peptide: fusion protein of mCerulean and FUS LCD
Keywordsamyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


membraneless organelle assembly / mRNA stabilization / intracellular membraneless organelle / regulation of RNA splicing / postsynaptic cytosol / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / presynaptic cytosol / mRNA Splicing - Major Pathway / RNA splicing ...membraneless organelle assembly / mRNA stabilization / intracellular membraneless organelle / regulation of RNA splicing / postsynaptic cytosol / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / presynaptic cytosol / mRNA Splicing - Major Pathway / RNA splicing / GABA-ergic synapse / mRNA 3'-UTR binding / transcription coregulator activity / molecular condensate scaffold activity / protein homooligomerization / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / glutamatergic synapse / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding
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 superfamily / Zinc finger RanBP2-type signature. / 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 superfamily / Zinc finger RanBP2-type signature. / 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 speciesAequorea victoria (jellyfish) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSun YP / Xia WC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: iScience / Year: 2022
Title: Molecular structure of an amyloid fibril formed by FUS low-complexity domain.
Authors: Yunpeng Sun / Shenqing Zhang / Jiaojiao Hu / Youqi Tao / Wencheng Xia / Jinge Gu / Yichen Li / Qin Cao / Dan Li / Cong Liu /
Abstract: FUS is a multifunctional nuclear protein which undergoes liquid-liquid phase separation in response to stress and DNA damage. Dysregulation of FUS dynamic phase separation leads to formation of ...FUS is a multifunctional nuclear protein which undergoes liquid-liquid phase separation in response to stress and DNA damage. Dysregulation of FUS dynamic phase separation leads to formation of pathological fibril closely associated with neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. In this study, we determined the cryo-EM structure of a cytotoxic fibril formed by the low-complexity (LC) domain of FUS at 2.9 Å resolution. The fibril structure exhibits a new and extensive serpentine fold consisting of three motifs incorporating together via a Tyr triad. FUS LC employs 91 residues to form an enlarged and stable fibril core via hydrophilic interaction and hydrogen bonds, which is distinct from most of previously determined fibrils commonly stabilized by hydrophobic interaction. Our work reveals the structural basis underlying formation of a cytotoxic and thermostable fibril of FUS LC and sheds light on understanding the liquid-to-solid phase transition of FUS in disease.
History
DepositionOct 20, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vqq
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vqq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32092.png

Downloads & links

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Map

FileDownload / File: emd_32092.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.060522124 - 0.09749564
Average (Standard dev.)0.00049027405 (±0.003939824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0610.0970.000

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Supplemental data

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Sample components

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Entire : Amyloid fibril formed by FUS low complexity domain

EntireName: Amyloid fibril formed by FUS low complexity domain
Components
  • Organelle or cellular component: Amyloid fibril formed by FUS low complexity domain
    • Protein or peptide: fusion protein of mCerulean and FUS LCD

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Supramolecule #1: Amyloid fibril formed by FUS low complexity domain

SupramoleculeName: Amyloid fibril formed by FUS low complexity domain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aequorea victoria (jellyfish)

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Macromolecule #1: fusion protein of mCerulean and FUS LCD

MacromoleculeName: fusion protein of mCerulean and FUS LCD / type: protein_or_peptide / ID: 1
Details: 6His-tagged mCerulean:(FPbase ID: J2JWA, Link: https://www.fpbase.org/protein/mcerulean/)
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.948352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMVSKG EELFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLTL KFICTTGKLP VPWPTLVTT LTWGVQCFAR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED G NILGHKLE ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMVSKG EELFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLTL KFICTTGKLP VPWPTLVTT LTWGVQCFAR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED G NILGHKLE YNAISDNVYI TADKQKNGIK ANFKIRHNIE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSKLSKDPN EK RDHMVLL EFVTAAGITL GMDELYKAGT MDPASNDYTQ QATQSYGAYP TQPGQGYSQQ SSQPYGQQSY SGYSQSTDTS GYG QSSYSS YGQSQNTGYG TQSTPQGYGS TGGYGSSQSS QSSYGQQSSY PGYGQQPAPS STSGSYGSSS QSSSYGQPQS GSYS QQPSY GGQQQSYGQQ QSYNPPQGYG QQNQYNSSSG GGGGGGGGGN YGQDQSSMSS GGGSGGGYGN QDQSGGGGSG GYGQQ DRG

UniProtKB: RNA-binding protein FUS

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.44 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171163
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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