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- PDB-9dei: Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1,... -

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Basic information

Entry
Database: PDB / ID: 9dei
TitleTrypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1)
Components
  • (RNA editing complex ...) x 2
  • (RNA-editing complex protein ...) x 2
  • KREPA2
  • KREPA5
  • KREPB5; RNA-editing catalytic complex core protein, B5
  • KREPB8; RNA editing catalytic complex core protein, B8
  • MP18 RNA editing complex protein, putative
  • MP90
  • tRNA-valine (anticodon AAC)
KeywordsRNA BINDING PROTEIN / RNA editing / tRNA / OB-fold / mitochondria
Function / homology
Function and homology information


mRNA editing complex / RNA nucleotide insertion / RNA nucleotide deletion / RNA modification / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mitochondrial RNA modification / kinetoplast / alpha-catenin binding / ribonuclease III activity / response to metal ion ...mRNA editing complex / RNA nucleotide insertion / RNA nucleotide deletion / RNA modification / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mitochondrial RNA modification / kinetoplast / alpha-catenin binding / ribonuclease III activity / response to metal ion / mRNA modification / RNA processing / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / mitochondrion / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA editing complex, structural subunit MP63 / RNA editing complex, nuclease subunit MP42 / RNA editing complex, structural subunit MP81 / RNA editing complex, subunit MP18 / : / RNA editing complex structural subunit MP81, C2H2 zinc finger / Ribonuclease III, endonuclease domain superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...RNA editing complex, structural subunit MP63 / RNA editing complex, nuclease subunit MP42 / RNA editing complex, structural subunit MP81 / RNA editing complex, subunit MP18 / : / RNA editing complex structural subunit MP81, C2H2 zinc finger / Ribonuclease III, endonuclease domain superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) / KREPA2 / KREPA5 / MP90 / Uncharacterized protein / RNA editing complex protein / MP18 RNA editing complex protein, putative / RNA editing complex protein MP46 ...GUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) / KREPA2 / KREPA5 / MP90 / Uncharacterized protein / RNA editing complex protein / MP18 RNA editing complex protein, putative / RNA editing complex protein MP46 / RNA-editing complex protein MP42 / RNA-editing complex protein MP81
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsLiu, Y.T. / Jih, J. / Zhou, Z.H. / Aphasizhev, R.
Funding support United States, China, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI152408 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI177658 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI113157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145249 United States
National Natural Science Foundation of China (NSFC)32570759 China
CitationJournal: Nature / Year: 2026
Title: Structural basis of the RNA-editing cascade in trypanosome mitochondria.
Authors: Yun-Tao Liu / Andres F Vacas / Jonathan Jih / Xiaojing Zhao / Clinton Yu / Jane K J Lee / Takuma Suematsu / Md Solayman / Hong Wang / Xiaorong Wang / Lan Huang / Liye Zhang / Inna ...Authors: Yun-Tao Liu / Andres F Vacas / Jonathan Jih / Xiaojing Zhao / Clinton Yu / Jane K J Lee / Takuma Suematsu / Md Solayman / Hong Wang / Xiaorong Wang / Lan Huang / Liye Zhang / Inna Aphasizheva / Z Hong Zhou / Ruslan Aphasizhev /
Abstract: The molecular mechanism of uridine insertion-and-deletion mRNA editing in trypanosome mitochondria has remained unclear because of the highly dynamic nature of the underlying multi-enzyme machinery. ...The molecular mechanism of uridine insertion-and-deletion mRNA editing in trypanosome mitochondria has remained unclear because of the highly dynamic nature of the underlying multi-enzyme machinery. Here, we define editosomes as supramolecular assemblies formed by the RNA-editing substrate-binding complex (RESC) and either RNA-editing catalytic complex 1 or 2 (RECC1 or RECC2), and present cryo-electron microscopy structures of the approximately 1-MDa RECC1 and RECC2. Resembling dragonflies, with a head, thorax-like core, tail and wings, these ribonucleoproteins mediate the uridine deletion and uridine insertion cascades, respectively. In each RECC, a tetrameric core containing one active and three inactive RNase III domains captures the guide RNA (gRNA)-mRNA duplex, while auxiliary zinc fingers distinguish deletion sites from insertion sites and position the substrate for mRNA cleavage (step I). Three peripheral oligonucleotide-binding-fold heterotetramers are flexibly attached to the core, forming a spatially adaptable reaction chamber. The tail recruits the exonuclease and uridylyltransferase that remove or add uridines (step II), whereas the wings, coordinated by an architectural tRNA, position RNA ligases to seal the edited mRNA (step III). Together, these structures reveal how gRNA-directed substrate recognition, mRNA cleavage, uridine deletion and insertion and ligation are integrated in a single macromolecular machine. This architecture defines the mechanism of information transfer in RNA editing.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Jul 1, 2026Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _em_admin.last_update
Revision 1.1Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update
Revision 2.1Jul 22, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.2Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KREPB5; RNA-editing catalytic complex core protein, B5
B: KREPB8; RNA editing catalytic complex core protein, B8
C: MP90
D: RNA editing complex protein MP46
E: MP18 RNA editing complex protein, putative
F: RNA-editing complex protein MP42
G: KREPA2
H: MP18 RNA editing complex protein, putative
I: RNA editing complex protein
J: MP18 RNA editing complex protein, putative
K: KREPA2
L: KREPA5
M: MP18 RNA editing complex protein, putative
N: RNA-editing complex protein MP42
O: RNA-editing complex protein MP81
P: MP18 RNA editing complex protein, putative
R: tRNA-valine (anticodon AAC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)672,81126
Polymers672,04817
Non-polymers7639
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 11 molecules ABCEHJMPGKL

#1: Protein KREPB5; RNA-editing catalytic complex core protein, B5


Mass: 43818.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427
#2: Protein KREPB8; RNA editing catalytic complex core protein, B8


Mass: 41881.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: C9ZW42
#3: Protein MP90


Mass: 90093.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: C9ZIA9
#5: Protein
MP18 RNA editing complex protein, putative


Mass: 18097.566 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: D0A2P0
#7: Protein KREPA2


Mass: 62983.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: A0A3L6L0V2
#9: Protein KREPA5


Mass: 19081.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: A0A3L6L2P3

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RNA editing complex ... , 2 types, 2 molecules DI

#4: Protein RNA editing complex protein MP46


Mass: 46525.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: Q86MV9
#8: Protein RNA editing complex protein


Mass: 23769.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: D0A2N9

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RNA-editing complex protein ... , 2 types, 3 molecules FNO

#6: Protein RNA-editing complex protein MP42


Mass: 42318.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: Q95W13
#10: Protein RNA-editing complex protein MP81


Mass: 81307.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: Q95W15

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RNA chain , 1 types, 1 molecules R

#11: RNA chain tRNA-valine (anticodon AAC)


Mass: 24480.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427

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Non-polymers , 4 types, 376 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#14: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1RECC1COMPLEXFrom T. brucei mitochondrial T2 isolate#1-#110NATURAL
2RECC1 coreCOMPLEXEndonuclease-containing heterotetrameric core#1-#41NATURAL
3RECC1 left wingCOMPLEXPeripheral tetramer of OB-fold-containing A-proteins (A2, A3, and two copies of A6)#5-#71NATURAL
4RECC1 right wingCOMPLEXPeripheral tetramer of OB-fold-containing A-proteins (A2, A4, A5, and A6)#5, #7-#91NATURAL
5RECC1 tailCOMPLEXPeripheral tetramer of OB-fold-containing A-proteins (A1, A3, and two copies of A6)#5-#6, #101NATURAL
6tRNACOMPLEXBridges RECC1 core and left wing#111NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrainOrganelle
21Trypanosoma brucei (eukaryote)5691Lister 427Mitochondria
32Trypanosoma brucei (eukaryote)5691Lister 427Mitochondria
43Trypanosoma brucei (eukaryote)5691Lister 427Mitochondria
54Trypanosoma brucei (eukaryote)5691Lister 427Mitochondria
65Trypanosoma brucei (eukaryote)5691Lister 427Mitochondria
76Trypanosoma brucei (eukaryote)5691Lister 427Mitochondria
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
160 mMPotassium chlorideKCl1
225 mMTris hydrochlorideTris-HCl1
310 mMMagnesium chlorideMgCl21
45 mMn-OctylglucosideOG1
51 mMCalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: From T. brucei mitochondrial T2 isolate
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Alignment procedure: COMA FREE / C2 aperture diameter: 50 µm / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS KRIOS / Mode: BRIGHT FIELD / Cs: 2.7 mm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDNominal defocus max (nm)Nominal defocus min (nm)Nominal magnification (X)
13000100081000
22800600130000
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of real images
11245GATAN K3 BIOQUANTUM (6k x 4k)23092
223.545FEI FALCON IV (4k x 4k)40988
EM imaging optics
Energyfilter nameIDImaging-IDEnergyfilter slit width (eV)
GIF Bioquantum1120
TFS Selectris X2210

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Processing

EM software
IDNameCategoryImaging-ID
1cryoSPARCparticle selection
2SerialEMimage acquisition1
4cryoSPARCCTF correction
7Cootmodel fitting
9ISOLDEmodel refinement
10PHENIXmodel refinement
11EPUimage acquisition2
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
Image processingDetails: Falcon 4i and K3 Bioquantum images were combined for processing.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 452724 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: Consensus map and focused refinement maps were combined to generate a composite map for final model refinement.

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