[English] 日本語
Yorodumi
- PDB-9z0h: Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9z0h
TitleTrypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2)
Components
  • (RNA editing complex protein ...) x 3
  • (RNA-editing complex protein ...) x 2
  • KREPA2
  • KREPA5
  • KREPB7
  • MP18 RNA editing complex protein, putative
  • RNA editing complex protein
  • tRNA-valine (anticodon AAC)
KeywordsRNA BINDING PROTEIN / RNA editing / tRNA / OB-fold / mitochondria
Function / homology
Function and homology information


RNA nucleotide insertion / RNA nucleotide deletion / mRNA editing complex / RNA modification / mitochondrial mRNA editing complex / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mitochondrial RNA modification / kinetoplast / alpha-catenin binding / ribonuclease III activity ...RNA nucleotide insertion / RNA nucleotide deletion / mRNA editing complex / RNA modification / mitochondrial mRNA editing complex / 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, C2H2 zinc finger / RNA editing complex, structural subunit MP81 / RNA editing complex, subunit MP18 / Ribonuclease III family domain profile. / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Zinc finger, C2H2 type ...RNA editing complex, structural subunit MP63 / RNA editing complex, nuclease subunit MP42 / : / RNA editing complex structural subunit MP81, C2H2 zinc finger / RNA editing complex, structural subunit MP81 / RNA editing complex, subunit MP18 / Ribonuclease III family domain profile. / Ribonuclease III domain / 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
RNA / RNA (> 10) / KREPA2 / KREPB7 / KREPA5 / RNA editing complex protein / MP18 RNA editing complex protein, putative / RNA editing complex protein MP44 / RNA editing complex protein MP46 / RNA editing complex protein MP61 ...RNA / RNA (> 10) / KREPA2 / KREPB7 / KREPA5 / RNA editing complex protein / MP18 RNA editing complex protein, putative / RNA editing complex protein MP44 / RNA editing complex protein MP46 / RNA editing complex protein MP61 / 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: 2.79 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: 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.
History
DepositionNov 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA editing complex protein MP44
B: KREPB7
C: RNA editing complex protein MP61
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
O: RNA-editing complex protein MP81
R: tRNA-valine (anticodon AAC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,40221
Polymers570,02614
Non-polymers3767
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA editing complex protein ... , 3 types, 3 molecules ACD

#1: Protein RNA editing complex protein MP44


Mass: 43818.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: Q86MV8
#3: Protein RNA editing complex protein MP61


Mass: 60867.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: Q86MW1
#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

-
Protein , 5 types, 8 molecules BEHJGKIL

#2: Protein KREPB7


Mass: 47253.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / References: UniProt: A0A3L6L1W9
#5: Protein MP18 RNA editing complex protein, putative


Mass: 18097.566 Da / Num. of mol.: 3 / 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
#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
#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

-
RNA-editing complex protein ... , 2 types, 2 molecules FO

#6: Protein RNA-editing complex protein MP42


Mass: 42318.461 Da / Num. of mol.: 1 / 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

-
RNA chain , 1 types, 1 molecules R

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


Mass: 24825.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Strain: Lister 427

-
Non-polymers , 3 types, 206 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.: 2 / Source method: obtained synthetically / Formula: Mg
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1RECC2COMPLEXFrom T. brucei mitochondrial T2 isolate#1-#110NATURAL
2RECC2 coreCOMPLEXEndonuclease-containing heterotetrameric core#1-#41NATURAL
3RECC2 left wingCOMPLEXPeripheral tetramer of OB-fold-containing A-proteins (A2, A3, and two copies of A6)#5-#71NATURAL
4RECC2 right wingCOMPLEXPeripheral tetramer of OB-fold-containing A-proteins (A2, A4, A5, and A6)#8, #5, #7, #91NATURAL
5tRNACOMPLEXBridges RECC2 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
75Trypanosoma 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

-
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

-
Processing

EM software
IDNameCategoryImaging-ID
1cryoSPARCparticle selection
2SerialEMimage acquisition1
4cryoSPARCCTF correction
7Cootmodel fitting
9EPUimage acquisition2
10ISOLDEmodel refinement
11PHENIXmodel refinement
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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 496750 / 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.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more