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- PDB-8fnf: Cryo-EM structure of RNase-untreated RESC-C in trypanosomal RNA e... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fnf | ||||||||||||
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Title | Cryo-EM structure of RNase-untreated RESC-C in trypanosomal RNA editing | ||||||||||||
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![]() | RNA BINDING PROTEIN/RNA / HEAT repeat / trypanosoma / RNA editing substrate binding complex / gRNA / RNA BINDING PROTEIN-RNA complex | ||||||||||||
Function / homology | ![]() regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / chloroplast rRNA processing / RNA modification / ribonucleoprotein granule / phytanoyl-CoA dioxygenase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / RNA metabolic process ...regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / chloroplast rRNA processing / RNA modification / ribonucleoprotein granule / phytanoyl-CoA dioxygenase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / RNA metabolic process / kinetoplast / cytidine to uridine editing / mRNA stabilization / post-transcriptional regulation of gene expression / RNA processing / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Liu, S. / Wang, H. / Li, X. / Zhang, F. / Lee, J.K.J. / Li, Z. / Yu, C. / Zhao, X. / Hu, J.J. / Suematsu, T. ...Liu, S. / Wang, H. / Li, X. / Zhang, F. / Lee, J.K.J. / Li, Z. / Yu, C. / Zhao, X. / Hu, J.J. / Suematsu, T. / Alvarez-Cabrera, A.L. / Liu, Q. / Zhang, L. / Huang, L. / Aphasizheva, I. / Aphasizhev, R. / Zhou, Z.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / ...Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou / ![]() ![]() Abstract: In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial ...In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 390.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 66.8 KB | Display | |
Data in CIF | ![]() | 101.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 29311MC ![]() 8fn4C ![]() 8fn6C ![]() 8fncC ![]() 8fniC ![]() 8fnkC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 2 types, 2 molecules mg
#1: RNA chain | Mass: 6455.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 4968.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Mitochondrial RNA binding ... , 2 types, 2 molecules 58
#3: Protein | Mass: 34727.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 61109.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RAP domain-containing ... , 2 types, 2 molecules 610
#4: Protein | Mass: 57823.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#7: Protein | Mass: 60563.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules 714
#5: Protein | Mass: 18669.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#8: Protein | Mass: 41293.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RESC5-tagged isolate without RNase treatment / Type: COMPLEX Details: CTS-tagged RESC5 purified from RNase-untreated mitochondrial extract by tandem affinity procedure Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239134 / Symmetry type: POINT |