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- EMDB-0698: 120kV MicroED structure of FUS (37-42) SYSGYS solved from merged ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0698
Title120kV MicroED structure of FUS (37-42) SYSGYS solved from merged datasets at 0.60 A
Map data2Fo-Fc map
Sample
  • Complex: FUS LC RAC1
    • Protein or peptide: RNA-binding protein FUS
  • Ligand: water
KeywordsFUS / MicroED / Ultrahigh resolution / RNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / 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 / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / 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)
Methodelectron crystallography / cryo EM / Resolution: 0.6 Å
AuthorsZhou H / Luo F
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501902 China
Ministry of Science and Technology (China)2016YFA0501102 China
National Natural Science Foundation of China31570730 China
National Natural Science Foundation of China91853113 China
CitationJournal: Anal Chem / Year: 2019
Title: Programming Conventional Electron Microscopes for Solving Ultrahigh-Resolution Structures of Small and Macro-Molecules.
Authors: Heng Zhou / Feng Luo / Zhipu Luo / Dan Li / Cong Liu / Xueming Li /
Abstract: Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of ...Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lack of automated data collection methods. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with a single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ∼0.60 Å with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED and demonstrates the capability of the low-end 120 kV microscope with a CCD camera in solving ultrahigh resolution structures of both organic compounds and biological macromolecules.
History
DepositionJul 20, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kj3
  • Surface level: 1
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0698.png

Downloads & links

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Map

FileDownload / File: emd_0698.map.gz / Format: CCP4 / Size: 10.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2Fo-Fc map
Voxel sizeX: 0.1425 Å / Y: 0.14594 Å / Z: 0.14658 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.040721 - 12.839497
Average (Standard dev.)-0.000456111 (±0.9876727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-20-50-35
Dimensions105208131
Spacing131105208
CellA: 18.6675 Å / B: 15.323701 Å / C: 30.48864 Å
α: 90.0 ° / β: 90.307 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.142496183206110.145942857142860.14658173076923
M x/y/z131105208
origin x/y/z0.0000.0000.000
length x/y/z18.66715.32430.489
α/β/γ90.00090.30790.000
start NX/NY/NZ-35-20-50
NX/NY/NZ131105208
MAP C/R/S321
start NC/NR/NS-50-20-35
NC/NR/NS208105131
D min/max/mean-2.04112.839-0.000

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Supplemental data

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Additional map: Fo-Fc map

Fileemd_0698_additional.map
AnnotationFo-Fc map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Fo-Fc map

Fileemd_0698_additional_1.map
AnnotationFo-Fc map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FUS LC RAC1

EntireName: FUS LC RAC1
Components
  • Complex: FUS LC RAC1
    • Protein or peptide: RNA-binding protein FUS
  • Ligand: water

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Supramolecule #1: FUS LC RAC1

SupramoleculeName: FUS LC RAC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Macromolecule #1: RNA-binding protein FUS

MacromoleculeName: RNA-binding protein FUS / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 662.648 Da
SequenceString:
SYSGYS

UniProtKB: RNA-binding protein FUS

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 500 mm
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 0.05 e/Å2

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Image processing

Crystallography statisticsNumber intensities measured: 46057 / Number structure factors: 5850 / Fourier space coverage: 78.41 / R sym: 0.278 / R merge: 0.278 / Overall phase error: 44.58 / Overall phase residual: 1 / Phase error rejection criteria: 60 / High resolution: 0.6 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.6 Å / Shell - Low resolution: 0.62 Å / Shell - Number structure factors: 474 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 66.76 / Shell - Multiplicity: 3.94
Final reconstructionResolution.type: BY AUTHOR / Resolution: 0.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-6kj3:
120kV MicroED structure of FUS (37-42) SYSGYS solved from merged datasets at 0.60 A

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