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 2.1 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 

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


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
KREPB5; RNA-editing catalytic complex core protein, B5384Trypanosoma bruceiMutation(s): 0 
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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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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MP90818Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for C9ZIA9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
Explore C9ZIA9 
Go to UniProtKB:  C9ZIA9
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UniProt GroupC9ZIA9
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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 D0A2P0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
Explore D0A2P0 
Go to UniProtKB:  D0A2P0
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UniProt GroupD0A2P0
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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 A0A3L6L0V2 (Trypanosoma brucei equiperdum)
Explore A0A3L6L0V2 
Go to UniProtKB:  A0A3L6L0V2
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UniProt GroupA0A3L6L0V2
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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 D0A2N9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
Explore D0A2N9 
Go to UniProtKB:  D0A2N9
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UniProt GroupD0A2N9
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
KREPA5169Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L2P3 (Trypanosoma brucei equiperdum)
Explore A0A3L6L2P3 
Go to UniProtKB:  A0A3L6L2P3
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UniProt GroupA0A3L6L2P3
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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 
Go to UniProtKB:  Q95W15
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UniProt GroupQ95W15
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Reference Sequence
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(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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View more in-depth experimental data

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