9DEI | pdb_00009dei

Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1)

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Trypanosoma brucei
  • Mutation(s): No 

  • Deposited: 2024-08-29 Released: 2026-01-21 
  • Deposition Author(s): Liu, Y.T., Jih, J., Zhou, Z.H., Aphasizhev, R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9DEI

This is version 2.2 of the entry. See complete history

Literature

Structural basis of the RNA-editing cascade in trypanosome mitochondria.

Liu, Y.T.Vacas, A.F.Jih, J.Zhao, X.Yu, C.Lee, J.K.J.Suematsu, T.Solayman, M.Wang, H.Wang, X.Huang, L.Zhang, L.Aphasizheva, I.Zhou, Z.H.Aphasizhev, R.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10831-x
  • Primary Citation Related Structures: 
    9DEI, 9Z0H

  • PubMed Abstract: 

    The molecular mechanism of uridine insertion-and-deletion mRNA editing in trypanosome mitochondria 1-4 has remained unclear because of the highly dynamic nature of the underlying multi-enzyme machinery 5 . 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) 6 , 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.


  • Organizational Affiliation
    • Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 672.81 kDa 
  • Atom Count: 28,120 
  • Modeled Residue Count: 3,381 
  • Deposited Residue Count: 5,989 
  • Unique protein chains: 10
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
KREPB5; RNA-editing catalytic complex core protein, B5384Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q86MV8 (Trypanosoma brucei)
Explore Q86MV8 
Go to UniProtKB:  Q86MV8
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UniProt GroupQ86MV8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KREPB8; RNA editing catalytic complex core protein, B8368Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for C9ZW42 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
Explore C9ZW42 
Go to UniProtKB:  C9ZW42
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UniProt GroupC9ZW42
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MP90818Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q86MW3 (Trypanosoma brucei)
Explore Q86MW3 
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UniProt GroupQ86MW3
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA editing complex protein MP46414Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q86MV9 (Trypanosoma brucei)
Explore Q86MV9 
Go to UniProtKB:  Q86MV9
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UniProt GroupQ86MV9
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
MP18 RNA editing complex protein, putative
E, H, J, M, P
164Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q0VJ90 (Trypanosoma brucei)
Explore Q0VJ90 
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UniProt GroupQ0VJ90
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-editing complex protein MP42
F, N
393Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q95W13 (Trypanosoma brucei)
Explore Q95W13 
Go to UniProtKB:  Q95W13
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UniProt GroupQ95W13
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
KREPA2
G, K
587Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q95W14 (Trypanosoma brucei)
Explore Q95W14 
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UniProt GroupQ95W14
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA editing complex protein218Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q86MW0 (Trypanosoma brucei)
Explore Q86MW0 
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UniProt GroupQ86MW0
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
KREPA5169Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q57YG2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57YG2 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-editing complex protein MP81762Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q95W15 (Trypanosoma brucei)
Explore Q95W15 
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UniProt GroupQ95W15
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 11
MoleculeChains LengthOrganismImage
tRNA-valine (anticodon AAC)Q [auth R]76Trypanosoma brucei
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP

Query on 5GP



Download:Ideal Coordinates CCD File
Z [auth R]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
R [auth B],
V [auth C],
W [auth D],
X [auth K],
Y [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
S [auth C],
T [auth C],
U [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI101057
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1AI152408
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI177658
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI113157
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM145249
National Natural Science Foundation of China (NSFC)China32570759

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 2.0: 2026-07-01
    Changes: Atomic model, Data collection
  • Version 2.1: 2026-07-22
    Changes: Data collection, Database references
  • Version 2.2: 2026-08-05
    Changes: Data collection, Database references