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- PDB-6kj3: 120kV 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: 6kj3 | |||||||||||||||
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Title | 120kV MicroED structure of FUS (37-42) SYSGYS solved from merged datasets at 0.60 A | |||||||||||||||
![]() | RNA-binding protein FUS | |||||||||||||||
![]() | RNA BINDING PROTEIN / FUS / MicroED / Ultrahigh resolution | |||||||||||||||
Function / homology | ![]() mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / transcription coregulator activity / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding ...mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / transcription coregulator activity / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / protein homooligomerization / transcription coactivator activity / amyloid fibril formation / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.6 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 | ![]() | 11.5 KB | Display | ![]() |
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PDB format | ![]() | 6.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0698MC ![]() 0696C ![]() 0697C ![]() 0699C ![]() 6kj1C ![]() 6kj2C ![]() 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: 9.2 Data #1: 120kV 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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1 |
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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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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Data collection
Microscopy | Model: FEI TECNAI 12 / Date: Mar 22, 2018 | |||||||||||||||||||||||||
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Electron gun | Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM | |||||||||||||||||||||||||
Electron lens | Mode: DIFFRACTION | |||||||||||||||||||||||||
Image recording | Electron dose: 0.05 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) | |||||||||||||||||||||||||
EM diffraction | Camera length: 500 mm | |||||||||||||||||||||||||
EM diffraction shell | Resolution: 0.6→0.62 Å / Fourier space coverage: 66.76 % / Multiplicity: 3.94 / Num. of structure factors: 474 / Phase residual: 1 ° | |||||||||||||||||||||||||
EM diffraction stats | Fourier space coverage: 78.41 % / High resolution: 0.6 Å / Num. of intensities measured: 46057 / Num. of structure factors: 5850 / Phase error: 44.58 ° / Phase residual: 1 ° / Phase error rejection criteria: 60 / Rmerge: 0.278 / Rsym: 0.278 | |||||||||||||||||||||||||
Reflection twin |
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Processing
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90.31 ° / ∠γ: 90 ° / A: 17.1 Å / B: 4.67 Å / C: 17.59 Å / Space group name: P1211 / Space group num: 4 | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 0.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: RECIPROCAL | ||||||||||||||||||||||||
Refinement | Resolution: 0.6→8.55 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.839 / SU B: 0.589 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 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: 1.88 Å2 / Biso mean: 0.799 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 0.6→8.55 Å
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LS refinement shell | Resolution: 0.6→0.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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