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- EMDB-46791: Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1,... -

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Basic information

Entry
Database: EMDB / ID: EMD-46791
TitleTrypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1), composite map
Map dataRNA-editing catalytic complex 1 (RECC1), composite map
Sample
  • Complex: RECC1
    • Complex: RECC1 core
      • Protein or peptide: x 4 types
    • Complex: RECC1 left wing
      • Protein or peptide: x 3 types
    • Complex: RECC1 right wing
      • Protein or peptide: x 2 types
    • Complex: RECC1 tail
      • Protein or peptide: x 1 types
    • Complex: tRNA
      • RNA: x 1 types
  • Ligand: x 4 types
KeywordsRNA editing / tRNA / OB-fold / mitochondria / RNA BINDING PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsLiu YT / Jih J / Zhou ZH / Aphasizhev R
Funding support United States, China, 7 items
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 YT / Vacas AF / Jih J / Zhao X / Yu C / Lee JKJ / Suematsu T / Solayman M / Wang H / Wang X / Huang L / Zhang L / Aphasizheva I / Zhou ZH / Aphasizhev R
History
DepositionAug 29, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46791.png

Downloads & links

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Map

FileDownload / File: emd_46791.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA-editing catalytic complex 1 (RECC1), composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-39.675249999999998 - 71.537009999999995
Average (Standard dev.)0.006750229 (±1.0837945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RECC1

EntireName: RECC1
Components
  • Complex: RECC1
    • Complex: RECC1 core
      • Protein or peptide: KREPB5; RNA-editing catalytic complex core protein, B5
      • Protein or peptide: KREPB8; RNA editing catalytic complex core protein, B8
      • Protein or peptide: MP90
      • Protein or peptide: RNA editing complex protein MP46
    • Complex: RECC1 left wing
      • Protein or peptide: MP18 RNA editing complex protein, putative
      • Protein or peptide: RNA-editing complex protein MP42
      • Protein or peptide: KREPA2
    • Complex: RECC1 right wing
      • Protein or peptide: RNA editing complex protein
      • Protein or peptide: KREPA5
    • Complex: RECC1 tail
      • Protein or peptide: RNA-editing complex protein MP81
    • Complex: tRNA
      • RNA: tRNA-valine (anticodon AAC)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE
  • Ligand: water

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Supramolecule #1: RECC1

SupramoleculeName: RECC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 / Details: From T. brucei mitochondrial T2 isolate
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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Supramolecule #2: RECC1 core

SupramoleculeName: RECC1 core / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: Endonuclease-containing heterotetrameric core
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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Supramolecule #3: RECC1 left wing

SupramoleculeName: RECC1 left wing / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#7
Details: Peripheral tetramer of OB-fold-containing A-proteins (A2, A3, and two copies of A6)
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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Supramolecule #4: RECC1 right wing

SupramoleculeName: RECC1 right wing / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5, #7-#9
Details: Peripheral tetramer of OB-fold-containing A-proteins (A2, A4, A5, and A6)
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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Supramolecule #5: RECC1 tail

SupramoleculeName: RECC1 tail / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5-#6, #10
Details: Peripheral tetramer of OB-fold-containing A-proteins (A1, A3, and two copies of A6)
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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Supramolecule #6: tRNA

SupramoleculeName: tRNA / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #11 / Details: Bridges RECC1 core and left wing
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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Macromolecule #1: KREPB5; RNA-editing catalytic complex core protein, B5

MacromoleculeName: KREPB5; RNA-editing catalytic complex core protein, B5
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 43.818895 KDa
SequenceString: MRRAVVLHTA APMCALTGKC VEDWESHRKS FDMRIFELLK GRVTSPTEPL PIKQIYATIA NPCRLVEEFT CAKTTRRLGR LHTALSFLR RHNVLLHSLL FHVKETQTWN TTPDFDRLAL YGESSLRHEV RARTLRLFPG IDSETYAALT SSVLSEEALH G LFDRLLMK ...String:
MRRAVVLHTA APMCALTGKC VEDWESHRKS FDMRIFELLK GRVTSPTEPL PIKQIYATIA NPCRLVEEFT CAKTTRRLGR LHTALSFLR RHNVLLHSLL FHVKETQTWN TTPDFDRLAL YGESSLRHEV RARTLRLFPG IDSETYAALT SSVLSEEALH G LFDRLLMK ALVGEKPVGK MRDWSLTPNQ CGQMLCAIVG EMSWFAARTK ATDRTHNNAL FPPSDALILH VLCCHVLESL PA ELLYNVL EPKVQRIKEN WVNEPMSIPE QLHLKPRTIG SLSLSLVAKP LTEEEGRRKE VAVSAEKCQL SLTPERVIGS VRS TMLPRW NYKRFEERRY HILESDKRQV LPLAMSPVGR GDVSLASEQM PDERRRELVA LALGGRYR

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Macromolecule #2: KREPB8; RNA editing catalytic complex core protein, B8

MacromoleculeName: KREPB8; RNA editing catalytic complex core protein, B8
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 41.881055 KDa
SequenceString: MHRGPPALLH NVGVATRSKS FAASTKLPGR LTPLPSTSST LQPTNTLLSS SAGIASLRQL VSASTLTSTS TSGKKRVGSL DAHCRLLSR GTSADSYMPM TSRSFDVFEG NNKQAWLDLK TGWCHLCQEP LGATMGVHIG DRDHTNLQYF LFLYAAHGRR W SSEEVLRS ...String:
MHRGPPALLH NVGVATRSKS FAASTKLPGR LTPLPSTSST LQPTNTLLSS SAGIASLRQL VSASTLTSTS TSGKKRVGSL DAHCRLLSR GTSADSYMPM TSRSFDVFEG NNKQAWLDLK TGWCHLCQEP LGATMGVHIG DRDHTNLQYF LFLYAAHGRR W SSEEVLRS CLATAPTVHN YATRHTTWDH LHVMDDALRR AELEALLFHL THPPQQALSH VLQGRSPLGF WYSGERMWKL RI SRLVTQV FPPISAGMMT NFTQKCWGRS NGERMYDALR LQRIKAYYGW QPYESKEKKA FFVRQLLWEL LSVEVRDEVD ELT KHMADL ALRRMAFEMI FLQSMEYMHK VQYVYDLMGR PTVDELAAMN LL

UniProtKB: Uncharacterized protein

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Macromolecule #3: MP90

MacromoleculeName: MP90 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 90.093039 KDa
SequenceString: MGLHWPLARS SNWCHMRALS NEHLRRRVGA AVRSIASTAP CFALERVEVA HSHAYSRRGV TVGFTSSSSS PSGKTGSGGL SPASQSLHS SSSFDASNGD VLANYVNFVA DDATGPAATK ENGAQPMRSL RSASAVENLL FTDAAKNYCR LCMEEVQVTP K AHISTPYR ...String:
MGLHWPLARS SNWCHMRALS NEHLRRRVGA AVRSIASTAP CFALERVEVA HSHAYSRRGV TVGFTSSSSS PSGKTGSGGL SPASQSLHS SSSFDASNGD VLANYVNFVA DDATGPAATK ENGAQPMRSL RSASAVENLL FTDAAKNYCR LCMEEVQVTP K AHISTPYR GSHTNHTCRE VVLDSLALLA IRGYPIDDVY FVWADTLYQS SVFQRIPELV SPRWTVDKRS EVLAKILFML KD MGVIDIS LAAQAPDLFD NTAQQVHHRR RVAFERLEYI GDNSWGNHLS NRMMLLFPDR QWTYSQNAYT FNCFRDACEM NVT LEFMFD TLRVGELLPP GVREKLGTGK IKADVVEAVI GELHVTLWGL EPQLYDSVCF VEINGVGEAR LAALVQHCLT EIYD LIVLS YVQELSGSAV PLAKQIAADR IWNSVYPPVR KAKDRAPGGR KSRSTVVNVV GVGEVRQLPS LPSLFPAASK RPTRA PHPL RRLRKLGEIP EETVCAGTNK DVFVHLIESY ERLDMLDDSL LPTLNMRRLQ DVQFSKLKRQ LVPSLSPAAL EELHNC KEL DAESVTPHKV GDKEVATDER VLDLEEVYFR DKYFDLFPTP LPNEVVTKEG DCDKRQSGAS TSRAVIISLP RGFDGSR PC NRAQLHMARN TIYPSLTERP AHSPTAGITK GDRVCLFSLS VYVPPDTKRP SAGVVTDKNL HFGEFAFHGV RIKGIECA S EPECISRRSN APGSDVGTSL NRSSWKEGGD NSCGTLTVED GTGENSVVGE DGDTGVNGGE GKAEDATGKH LLRAKWCRE NPFFPRASLP LLGISVGA

UniProtKB: MP90

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Macromolecule #4: RNA editing complex protein MP46

MacromoleculeName: RNA editing complex protein MP46 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 46.525059 KDa
SequenceString: MLRVENLRRS MTRLARHSLI RAVPFSPLSV GSSTDQTFGA PTRTPFRSHT CLLCDVSYES WGDHAESTTH IARHAICRTF VSPERHNAV MQQLWKHIRL DFGYVDEVTH KKEDRRRMRL ASTMRHLQEK GVLHHSLPRV TVDAQSEVSL TVESDSFVNY M FLGESFAR ...String:
MLRVENLRRS MTRLARHSLI RAVPFSPLSV GSSTDQTFGA PTRTPFRSHT CLLCDVSYES WGDHAESTTH IARHAICRTF VSPERHNAV MQQLWKHIRL DFGYVDEVTH KKEDRRRMRL ASTMRHLQEK GVLHHSLPRV TVDAQSEVSL TVESDSFVNY M FLGESFAR QETLDRVARL MPRAEALELS SIISFVLSKR RLAHFFDIFD MRKMVLNGDS SDDKASADGD VPPTIPRLQQ DG KAVILFS CLGELQMFSR RDRSHSVATR SAAEQLVLNV LGTHVMENII GELVHEALQT VVEEGTAVWR EHCGELKHKL FEG TKAASP PIATTPNPVS NSGGPEVTAD VNDQMWVDLC RLYVLDKNGS VPQLQPTVKR HSWHDVARAL TLELTVPNPV NKSA VFAAA APRLATKKK

UniProtKB: RNA editing complex protein MP46

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Macromolecule #5: MP18 RNA editing complex protein, putative

MacromoleculeName: MP18 RNA editing complex protein, putative / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 18.097566 KDa
SequenceString:
MLALTSRRLL LQQTFMRCCK SVNSVTLVGV VHDIQSGFVY EDAVTQFTLT TTSIDTTHPT QEVVVEKDHH TIRCFGELFS AEVKQKVKE GNVVCVNGRL RLSPQLEPSC NKHFYFPYIQ VQPPHGQVAV IHGDRRTVPA AVNPAVEDIK SEKEGAGGDQ S GVPS

UniProtKB: MP18 RNA editing complex protein, putative

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Macromolecule #6: RNA-editing complex protein MP42

MacromoleculeName: RNA-editing complex protein MP42 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 42.318461 KDa
SequenceString: MKRVTSHISR FLPLVLSQRG LSTYASPHVS SMRYYGATKC LLASTPDTPS FQCGECGKAF RLINALNHHI MTKHAGKAKA MMNKGGKLE EVNPEEIKNK PQGAMSQPTS PPPSSSTSGT EAASTSPTHS SFPGIPFSPV GGIGLVGTPV GAASHVVNTT T TAANSASG ...String:
MKRVTSHISR FLPLVLSQRG LSTYASPHVS SMRYYGATKC LLASTPDTPS FQCGECGKAF RLINALNHHI MTKHAGKAKA MMNKGGKLE EVNPEEIKNK PQGAMSQPTS PPPSSSTSGT EAASTSPTHS SFPGIPFSPV GGIGLVGTPV GAASHVVNTT T TAANSASG NALSDENADK KTFVCTICQK TFRLEAALQH HYQAKHNMEM PTSSSSSGGA SAQPVLQGGA TTAGVGSVGF SH TEEETGR SAMGTQYVHS QETILPQAPQ YHLDVAPNAP EEGEVAAHWR CVNHCVMLGV VQNIQEGFVF EDKVLQFTLI TDF EGPSPG DPDKDFHTVR VFDSDYSSRV KEQLRDGEWF LVTGRLRMVP QYDGSMRKYY HYPVIQVHPG CGSVLKV

UniProtKB: RNA-editing complex protein MP42

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Macromolecule #7: KREPA2

MacromoleculeName: KREPA2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 62.983031 KDa
SequenceString: MYRRFFRSAA VKHLGTTSAQ CLMRATKYPC GAMCRNASSC HPQTLGYQQR FQSTTDKKFH CSVCKKPFRL EMAAKLHLQQ AHGGDGSVE AGPGPGVEAS SVNVVSTPVP SPISPVERTF VDEEERRPRR MRPTPKPLHQ PDRDIPAAAM EEMLGVWDKI G LNRLEGNF ...String:
MYRRFFRSAA VKHLGTTSAQ CLMRATKYPC GAMCRNASSC HPQTLGYQQR FQSTTDKKFH CSVCKKPFRL EMAAKLHLQQ AHGGDGSVE AGPGPGVEAS SVNVVSTPVP SPISPVERTF VDEEERRPRR MRPTPKPLHQ PDRDIPAAAM EEMLGVWDKI G LNRLEGNF VHSTMVMKVF AAPPDVSEIP LYEHVAPEGE NPFDSLDHMT TGTVDATYVG HDAFAEVDLV DPFVAAPDQT LN PFRAGKV RNPFTRISPT QREVVKPLQP PQPKEEPLKA PVTPFGQLPM FGQTREPSAS FAAAAVSVQA AANPNEVSSP FAA AVSSSP FVGQVASPFA PAQDVAGSPF EASPCAASSP FVTAGGQETS PFAAPSTPAS FGQGSLFPPM GTGAPGFTAI TETE QRQQE LEHGCPTCGK KFSTFEGAAM HSKSKHGIVL ESKKVKDRLN RKGVPDLPAY VPSPVDLSST SPFGTRSAIG ASWAE TELI PHAQCVSNIT IVGRVLDVSQ ASENVSHVTV FVEGERSGEE ETLTLCCFGE VSQKIRGTLK RNATIFASGT LRLHPV YEA SNNKYYVSPV VHVSMPTGTL AVIT

UniProtKB: KREPA2

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Macromolecule #8: RNA editing complex protein

MacromoleculeName: RNA editing complex protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 23.769062 KDa
SequenceString: MWVRSLLLCI RRDPLQRAVD VAYASGMLLG SGSSRGTTHF SETTAFTSSN FAADLRGGRV GLAGDGGTKC EDRNGELVRG RIQFASRCA EGPFVGASPT VTSCAHIEGV VRQVECGYVG GDRVLQFIIE VEEVPASGGT PMRLPLAVRW RPGSEVAQNR M DEWQKEME ...String:
MWVRSLLLCI RRDPLQRAVD VAYASGMLLG SGSSRGTTHF SETTAFTSSN FAADLRGGRV GLAGDGGTKC EDRNGELVRG RIQFASRCA EGPFVGASPT VTSCAHIEGV VRQVECGYVG GDRVLQFIIE VEEVPASGGT PMRLPLAVRW RPGSEVAQNR M DEWQKEME RLVGRRVLAS GRLQVEECFD SGSRRLYKTP SLVLPATSTV EMISLQELEC

UniProtKB: RNA editing complex protein

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Macromolecule #9: KREPA5

MacromoleculeName: KREPA5 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 19.081924 KDa
SequenceString:
MFSSTFRRLA IRPLNRVTMV GAMHDIQVGF LDRCSVFQFT LTCTVLDFQK VAEPQPKSPG SLPSSTRTAP NANGEEVEKH INKEQYTVR CLGSEAYTEA LKNYLDDGCI VRVIGRLKTT EVVDAGKKQP FPCIIVEQGR WSTVSLVHSL RKQRRDWQLQ N ILTSVATL E

UniProtKB: KREPA5

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Macromolecule #10: RNA-editing complex protein MP81

MacromoleculeName: RNA-editing complex protein MP81 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 81.307188 KDa
SequenceString: MRRLTRRSDR LCGKGNGGSC LQMSPTHVGA VVTWSLNRLM PLHTRTIPLR CSLPTPESGT TEPRELCFYE TFELTGEDVH YLLLHEAHV KHGVLLNVPP QLAPNGTPPE VPEVIMPAAQ LERMGGMKLA YEPTHLPPPL HTTGARQLVL DESFYTTPTK E KKATTTAV ...String:
MRRLTRRSDR LCGKGNGGSC LQMSPTHVGA VVTWSLNRLM PLHTRTIPLR CSLPTPESGT TEPRELCFYE TFELTGEDVH YLLLHEAHV KHGVLLNVPP QLAPNGTPPE VPEVIMPAAQ LERMGGMKLA YEPTHLPPPL HTTGARQLVL DESFYTTPTK E KKATTTAV SHVSESTAAS GGRGGASATA AGTALPPRLP PDPTMKFHCS ACGKAFRLKF SADHHVKLNH GSDPKAAVVD GP GEGGLLG GAVTITTAKV AKHSSSAASG TASRAGDSAT LDVKQQPDPQ KELSASGISA VKIPYSKAVL SLPDDELVDE LLI DVWDAV AAQRDDVPKS NSANIFLPFA SVVTGTADRR KEMEAVARPT ARATPEGAAP GIKRPGAMAG GAVAVGKGRS GGQI LPIRE LIKKYPNPFG DSPNAAVQDL ENEPLNPFLP EEELAAQLQV ACEEDTVVTP SACTTDVSTG SVIGKKGSLE KLKEK LRGT RPSMAASAAK RRFTCPICVE KQQTLQQQQS ENVGSGFCTD IPSFRLLDAL LDHVESVHGE ELTEDQLREL YAKQRQ STL YPQKSSTGDG AGSRETPDDS EKKEGSVGNT SMDELKSLPE EVRRVVPPAP VEQDALAVHI RAGSNALMIG RIADVQH GF LGAMTVTQYV LEVDGDERIN SKGVTTPASA CTPDPASTKA VEAKGEEGEV VEPEKEFIVI RCMGDNFPAS LLKDQVKL G SRVLVQGTLR MNRHVDDVSK RLHAYPFIQV VPPLGYVKVV G

UniProtKB: RNA-editing complex protein MP81

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Macromolecule #11: tRNA-valine (anticodon AAC)

MacromoleculeName: tRNA-valine (anticodon AAC) / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 24.480467 KDa
SequenceString:
CGCUGAUGGU CUAGGUGGUU AUGACGUCGC UUUAACACGG CGAAGGUCUC GGGUUCGAGU CCCGAUCGGC GUACCA

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #13: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 13 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #14: GUANOSINE-5'-MONOPHOSPHATE

MacromoleculeName: GUANOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: 5GP
Molecular weightTheoretical: 363.221 Da
Chemical component information

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

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Macromolecule #15: water

MacromoleculeName: water / type: ligand / ID: 15 / Number of copies: 367 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Component:
ConcentrationFormulaName
60.0 mMKClPotassium chloride
25.0 mMTris-HClTris hydrochloride
10.0 mMMgCl2Magnesium chloride
5.0 mMOGn-Octylglucoside
1.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsFrom T. brucei mitochondrial T2 isolate

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 23092 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 40988 / Average exposure time: 3.5 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID2
DetailsFalcon 4i and K3 Bioquantum images were combined for processing.
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 452724
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

DetailsConsensus map and focused refinement maps were combined to generate a composite map for final model refinement.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9dei:
Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1)

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