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- PDB-6kj1: 200kV MicroED structure of FUS (37-42) SYSGYS solved from merged ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kj1 | |||||||||||||||
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Title | 200kV MicroED structure of FUS (37-42) SYSGYS solved from merged datasets at 0.65 A | |||||||||||||||
![]() | RNA-binding protein FUS | |||||||||||||||
![]() | RNA BINDING PROTEIN / FUS / MicroED / Ultrahigh resolution | |||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.65 Å | |||||||||||||||
![]() | Zhou, H. / Luo, F. / Luo, Z. / Li, D. / Liu, C. / Li, X. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 11.4 KB | Display | ![]() |
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PDB format | ![]() | 6.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 688.6 KB | Display | ![]() |
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Full document | ![]() | 688.3 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0696MC ![]() 0697C ![]() 0698C ![]() 0699C ![]() 6kj2C ![]() 6kj3C ![]() 6kj4C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 9.5 Data #1: 200kV MicroED data of FUS (37-42) SYSGYS [diffraction images]) |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 662.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
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Sample preparation
Component | Name: FUS LC RAC1 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES |
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Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Data collection
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Mar 16, 2018 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 0.05 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
EM diffraction | Camera length: 520 mm |
EM diffraction shell | Resolution: 0.65→0.67 Å / Fourier space coverage: 46.02 % / Multiplicity: 2.96 / Num. of structure factors: 318 / Phase residual: 1 ° |
EM diffraction stats | Fourier space coverage: 77.56 % / High resolution: 0.65 Å / Num. of intensities measured: 56923 / Num. of structure factors: 5476 / Phase error: 29.78 ° / Phase residual: 1 ° / Phase error rejection criteria: 60 / Rmerge: 0.22 / Rsym: 0.22 |
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Processing
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 91 ° / ∠γ: 90 ° / A: 18.21 Å / B: 4.93 Å / C: 18.77 Å / Space group name: P1211 / Space group num: 4 | ||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||
3D reconstruction | Resolution: 0.65 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: RECIPROCAL | ||||||||||||||||||||
Refinement | Resolution: 0.65→6.59 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.481 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.017 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||
Displacement parameters | Biso max: 2.99 Å2 / Biso min: 1.46 Å2
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Refinement step | Cycle: final / Resolution: 0.65→6.59 Å
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LS refinement shell | Resolution: 0.65→0.685 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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