9Z0H | pdb_00009z0h

Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2)

PDB DOI: https://doi.org/10.2210/pdb9Z0H/pdb
EM Map EMD-73706: EMDB EMDataResource
NAKB: 9Z0H

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

Deposited: 2025-11-01 Released: 2026-07-22
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: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 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

Macromolecule Content

Total Structure Weight: 570.4 kDa
Atom Count: 23,367
Modeled Residue Count: 2,791
Deposited Residue Count: 5,032
Unique protein chains: 10
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA editing complex protein MP44	A	384	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q86MV8 (Trypanosoma brucei) Explore Q86MV8 Go to UniProtKB: Q86MV8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86MV8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KREPB7	B	411	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for A0A3L6L1W9 (Trypanosoma brucei equiperdum) Explore A0A3L6L1W9 Go to UniProtKB: A0A3L6L1W9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3L6L1W9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA editing complex protein MP61	C	538	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q86MW1 (Trypanosoma brucei) Explore Q86MW1 Go to UniProtKB: Q86MW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86MW1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA editing complex protein MP46	D	414	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q86MV9 (Trypanosoma brucei) Explore Q86MV9 Go to UniProtKB: Q86MV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86MV9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
MP18 RNA editing complex protein, putative	E, H, J	164	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for D0A2P0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972)) Explore D0A2P0 Go to UniProtKB: D0A2P0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0A2P0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-editing complex protein MP42	F	393	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q95W13 (Trypanosoma brucei) Explore Q95W13 Go to UniProtKB: Q95W13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q95W13
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
KREPA2	G, K	587	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for A0A3L6L0V2 (Trypanosoma brucei equiperdum) Explore A0A3L6L0V2 Go to UniProtKB: A0A3L6L0V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3L6L0V2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA editing complex protein	I	218	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for D0A2N9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972)) Explore D0A2N9 Go to UniProtKB: D0A2N9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0A2N9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
KREPA5	L	169	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for A0A3L6L2P3 (Trypanosoma brucei equiperdum) Explore A0A3L6L2P3 Go to UniProtKB: A0A3L6L2P3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3L6L2P3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-editing complex protein MP81	M [auth O]	762	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q95W15 (Trypanosoma brucei) Explore Q95W15 Go to UniProtKB: Q95W15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q95W15
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 11
tRNA-valine (anticodon AAC)	N [auth R]	77	Trypanosoma brucei
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain U [auth O] SDF format, chain T [auth K] SDF format, chain S [auth D] SDF format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth O] MOL2 format, chain T [auth K] MOL2 format, chain S [auth D] MOL2 format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth O] mmCIF format, chain T [auth K] mmCIF format, chain S [auth D] mmCIF format, chain O [auth B]	O [auth B], R [auth C], S [auth D], T [auth K], U [auth O]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth K] Focus chain U [auth O] Interactions & Density Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth K] Focus chain U [auth O]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C]	P [auth C], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI101057
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	RO1AI152408
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI177658
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI113157
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM145249
National Natural Science Foundation of China (NSFC)	China	32570759

Revision History (Full details and data files)

Version 1.0: 2026-07-22
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9Z0H | pdb_00009z0h

Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2)

Literature

Structural basis of the RNA-editing cascade in trypanosome mitochondria

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)