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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


RNA nucleotide insertion / RNA nucleotide deletion / mRNA editing complex / RNA modification / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mitochondrial RNA modification / kinetoplast / alpha-catenin binding / ribonuclease III activity / mRNA modification ...RNA nucleotide insertion / RNA nucleotide deletion / mRNA editing complex / RNA modification / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mitochondrial RNA modification / kinetoplast / alpha-catenin binding / ribonuclease III activity / mRNA modification / response to metal ion / 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 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / 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 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / 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: To Be Published
Title: Structural basis of the mitochondrial RNA editing cascade in trypanosomes
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
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

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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
IDNameTypeDetailsEntity 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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