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- PDB-8fnk: Cryo-EM structure of RNase-untreated RESC-B in trypanosomal RNA e... -

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Basic information

Entry
Database: PDB / ID: 8fnk
TitleCryo-EM structure of RNase-untreated RESC-B in trypanosomal RNA editing
Components
  • (RNA-editing substrate-binding complex protein ...) x 9
  • gRNAGuide RNA
  • mRNAMessenger RNA
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 RNA modification / mitochondrial mRNA processing / RNA modification / ribonucleoprotein granule / mitochondrial mRNA editing complex / mitochondrial RNA processing / RNA metabolic process / cytidine to uridine editing / cytoplasmic side of mitochondrial outer membrane ...regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / ribonucleoprotein granule / mitochondrial mRNA editing complex / mitochondrial RNA processing / RNA metabolic process / cytidine to uridine editing / cytoplasmic side of mitochondrial outer membrane / kinetoplast / mRNA stabilization / post-transcriptional regulation of gene expression / RNA processing / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / nucleus / cytoplasm
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding protein / RNA-binding protein, putative / Mitochondrial RNA binding complex 1 subunit / Phytanoyl-CoA dioxygenase / Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding complex 1 subunit / Guide RNA binding protein / Mitochondrial RNA binding complex 1 subunit
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
m: mRNA
g: gRNA
5: RNA-editing substrate-binding complex protein 5 (RESC5)
6: RNA-editing substrate-binding complex protein 6 (RESC6)
7: RNA-editing substrate-binding complex protein 7 (RESC7)
8: RNA-editing substrate-binding complex protein 8 (RESC8)
9: RNA-editing substrate-binding complex protein 9 (RESC9)
10: RNA-editing substrate-binding complex protein 10 (RESC10)
11: RNA-editing substrate-binding complex protein 11 (RESC11)
13: RNA-editing substrate-binding complex protein 13 (RESC13)
14: RNA-editing substrate-binding complex protein 14 (RESC14)


Theoretical massNumber of molelcules
Total (without water)545,33311
Polymers545,33311
Non-polymers00
Water0
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 / Messenger RNA


Mass: 15963.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#2: RNA chain gRNA / Guide RNA


Mass: 13742.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)

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RNA-editing substrate-binding complex protein ... , 9 types, 9 molecules 5678910111314

#3: Protein RNA-editing substrate-binding complex protein 5 (RESC5)


Mass: 43469.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: RESC5 is tagged in situ in Trypanosoma brucei (5691), which shared the same native environment as other RESC proteins.
Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389F5
#4: Protein RNA-editing substrate-binding complex protein 6 (RESC6)


Mass: 57823.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57ZX7
#5: Protein RNA-editing substrate-binding complex protein 7 (RESC7)


Mass: 18669.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q384B4
#6: Protein RNA-editing substrate-binding complex protein 8 (RESC8)


Mass: 61109.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389W4
#7: Protein RNA-editing substrate-binding complex protein 9 (RESC9)


Mass: 96668.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q585T1
#8: Protein RNA-editing substrate-binding complex protein 10 (RESC10)


Mass: 60563.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57VS6
#9: Protein RNA-editing substrate-binding complex protein 11 (RESC11)


Mass: 103585.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57WL2
#10: Protein RNA-editing substrate-binding complex protein 13 (RESC13)


Mass: 32445.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389P7
#11: Protein RNA-editing substrate-binding complex protein 14 (RESC14)


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 without RNase treatment / Type: COMPLEX
Details: CTS-tagged RESC5 purified from RNase-untreated mitochondrial extract by tandem affinity procedure
Entity ID: #8-#11, #3-#7, #2, #1 / 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 FIELDBright-field microscopy / 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 K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62372 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00531598
ELECTRON MICROSCOPYf_angle_d0.62343202
ELECTRON MICROSCOPYf_dihedral_angle_d11.2015115
ELECTRON MICROSCOPYf_chiral_restr0.0395022
ELECTRON MICROSCOPYf_plane_restr0.0045245

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