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- PDB-8fnc: Cryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing -

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Basic information

Entry
Database: PDB / ID: 8fnc
TitleCryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing
Components
  • (Mitochondrial RNA binding ...) x 2
  • (RAP domain-containing ...) x 2
  • Phytanoyl-CoA dioxygenase family protein
  • RxLR effector protein
  • gRNA
  • mRNA
KeywordsRNA BINDING PROTEIN/RNA / HEAT repeat / trypanosoma / RNA editing substrate binding complex / gRNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of mitochondrial mRNA stability / mitochondrial mRNA processing / RNA modification / mitochondrial mRNA editing complex / RNA metabolic process / mitochondrial RNA modification / ribonucleoprotein granule / mitochondrial RNA processing / cytidine to uridine editing / kinetoplast ...regulation of mitochondrial mRNA stability / mitochondrial mRNA processing / RNA modification / mitochondrial mRNA editing complex / RNA metabolic process / mitochondrial RNA modification / ribonucleoprotein granule / mitochondrial RNA processing / cytidine to uridine editing / kinetoplast / mRNA stabilization / post-transcriptional regulation of gene expression / RNA processing / oxidoreductase activity / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Armadillo-type fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding protein / Mitochondrial RNA binding complex 1 subunit / Phytanoyl-CoA dioxygenase / Mitochondrial RNA binding complex 1 subunit / Guide RNA binding protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu, 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 United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI101057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: Science / Year: 2023
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
DepositionDec 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
m: mRNA
g: gRNA
5: Mitochondrial RNA binding protein
6: RAP domain-containing protein
7: RxLR effector protein
8: Mitochondrial RNA binding complex 1 subunit
10: RAP domain-containing protein
14: Phytanoyl-CoA dioxygenase family protein


Theoretical massNumber of molelcules
Total (without water)284,6648
Polymers284,6648
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules mg

#1: RNA chain mRNA


Mass: 5507.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#2: RNA chain gRNA


Mass: 4968.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)

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Mitochondrial RNA binding ... , 2 types, 2 molecules 58

#3: Protein Mitochondrial RNA binding protein


Mass: 34727.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389F5
#6: Protein Mitochondrial RNA binding complex 1 subunit


Mass: 61109.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389W4

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RAP domain-containing ... , 2 types, 2 molecules 610

#4: Protein RAP domain-containing protein


Mass: 57823.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57ZX7
#7: Protein RAP domain-containing protein


Mass: 60563.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57VS6

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Protein , 2 types, 2 molecules 714

#5: Protein RxLR effector protein


Mass: 18669.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q384B4
#8: Protein Phytanoyl-CoA dioxygenase family protein


Mass: 41293.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38EL9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RESC5-tagged isolate with RNase treatment / Type: COMPLEX
Details: CTS-tagged RESC5 purified from RNase-treated mitochondrial extract by tandem affinity procedure
Entity ID: all / Source: NATURAL
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414524 / Symmetry type: POINT

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