[English] 日本語
Yorodumi
- EMDB-0698: 120kV MicroED structure of FUS (37-42) SYSGYS solved from merged ... -

+
Open data


ID or keywords:

Loading...

-
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


membraneless organelle assembly / mRNA stabilization / intracellular membraneless organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / postsynaptic cytosol / 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 / Processing of Capped Intron-Containing Pre-mRNA / postsynaptic cytosol / positive regulation of double-strand break repair via homologous recombination / presynaptic cytosol / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity / molecular condensate scaffold activity / protein homooligomerization / GABA-ergic synapse / 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 / zinc ion binding / nucleoplasm / identical protein binding / nucleus
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 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

-
Structure visualization

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

emd_0698.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.14 Å/pix.
x 131 pix.
= 18.667 Å		0.15 Å/pix.
x 105 pix.
= 15.324 Å		0.15 Å/pix.
x 208 pix.
= 30.489 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.1425 Å / Y: 0.14594 Å / Z: 0.14658 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
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)

-
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)

-
Sample components

-
Entire : FUS LC RAC1

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

-
Supramolecule #1: FUS LC RAC1

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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 0.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more