[English] 日本語
Yorodumi
- EMDB-73706: Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73706
TitleTrypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2), composite map
Map dataRNA-editing catalytic complex 2 (RECC2), composite map
Sample
  • Complex: RECC2
    • Complex: RECC2 core
      • Protein or peptide: x 4 types
    • Complex: RECC2 left wing
      • Protein or peptide: x 3 types
    • Complex: RECC2 right wing
      • Protein or peptide: x 2 types
    • Complex: tRNA
      • RNA: x 1 types
    • Protein or peptide: x 1 types
  • Ligand: x 3 types
KeywordsRNA editing / tRNA / OB-fold / mitochondria / RNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA editing complex / RNA nucleotide insertion / RNA nucleotide deletion / RNA modification / mitochondrial mRNA editing complex / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / mitochondrial RNA modification / kinetoplast / alpha-catenin binding / ribonuclease III activity ...mRNA editing complex / RNA nucleotide insertion / RNA nucleotide deletion / 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 / RNA editing complex, subunit MP18 / : / RNA editing complex structural subunit MP81, C2H2 zinc finger / 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 / RNA editing complex, subunit MP18 / : / RNA editing complex structural subunit MP81, C2H2 zinc finger / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 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: Nature / Year: 2026
Title: Structural basis of the RNA-editing cascade in trypanosome mitochondria.
Authors: Yun-Tao Liu / Andres F Vacas / Jonathan Jih / Xiaojing Zhao / Clinton Yu / Jane K J Lee / Takuma Suematsu / Md Solayman / Hong Wang / Xiaorong Wang / Lan Huang / Liye Zhang / Inna ...Authors: Yun-Tao Liu / Andres F Vacas / Jonathan Jih / Xiaojing Zhao / Clinton Yu / Jane K J Lee / Takuma Suematsu / Md Solayman / Hong Wang / Xiaorong Wang / Lan Huang / Liye Zhang / Inna Aphasizheva / Z Hong Zhou / Ruslan Aphasizhev /
Abstract: The molecular mechanism of uridine insertion-and-deletion mRNA editing in trypanosome mitochondria has remained unclear because of the highly dynamic nature of the underlying multi-enzyme machinery. ...The molecular mechanism of uridine insertion-and-deletion mRNA editing in trypanosome mitochondria has remained unclear because of the highly dynamic nature of the underlying multi-enzyme machinery. Here, we define editosomes as supramolecular assemblies formed by the RNA-editing substrate-binding complex (RESC) and either RNA-editing catalytic complex 1 or 2 (RECC1 or RECC2), and present cryo-electron microscopy structures of the approximately 1-MDa RECC1 and RECC2. Resembling dragonflies, with a head, thorax-like core, tail and wings, these ribonucleoproteins mediate the uridine deletion and uridine insertion cascades, respectively. In each RECC, a tetrameric core containing one active and three inactive RNase III domains captures the guide RNA (gRNA)-mRNA duplex, while auxiliary zinc fingers distinguish deletion sites from insertion sites and position the substrate for mRNA cleavage (step I). Three peripheral oligonucleotide-binding-fold heterotetramers are flexibly attached to the core, forming a spatially adaptable reaction chamber. The tail recruits the exonuclease and uridylyltransferase that remove or add uridines (step II), whereas the wings, coordinated by an architectural tRNA, position RNA ligases to seal the edited mRNA (step III). Together, these structures reveal how gRNA-directed substrate recognition, mRNA cleavage, uridine deletion and insertion and ligation are integrated in a single macromolecular machine. This architecture defines the mechanism of information transfer in RNA editing.
History
DepositionNov 1, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73706.png

Downloads & links

-
Map

FileDownload / File: emd_73706.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA-editing catalytic complex 2 (RECC2), 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: 8.119999999999999
Minimum - Maximum-50.206642000000002 - 76.637659999999997
Average (Standard dev.)0.0025780422 (±1.0162212)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

+
Entire : RECC2

EntireName: RECC2
Components
  • Complex: RECC2
    • Complex: RECC2 core
      • Protein or peptide: RNA editing complex protein MP44
      • Protein or peptide: KREPB7
      • Protein or peptide: RNA editing complex protein MP61
      • Protein or peptide: RNA editing complex protein MP46
    • Complex: RECC2 left wing
      • Protein or peptide: MP18 RNA editing complex protein, putative
      • Protein or peptide: RNA-editing complex protein MP42
      • Protein or peptide: KREPA2
    • Complex: RECC2 right wing
      • Protein or peptide: RNA editing complex protein
      • Protein or peptide: KREPA5
    • Complex: tRNA
      • RNA: tRNA-valine (anticodon AAC)
    • Protein or peptide: RNA-editing complex protein MP81
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

+
Supramolecule #1: RECC2

SupramoleculeName: RECC2 / 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

+
Supramolecule #2: RECC2 core

SupramoleculeName: RECC2 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

+
Supramolecule #3: RECC2 left wing

SupramoleculeName: RECC2 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

+
Supramolecule #4: RECC2 right wing

SupramoleculeName: RECC2 right wing / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8, #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

+
Supramolecule #5: tRNA

SupramoleculeName: tRNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #11 / Details: Bridges RECC2 core and left wing
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

+
Macromolecule #1: RNA editing complex protein MP44

MacromoleculeName: RNA editing complex protein MP44 / 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

UniProtKB: RNA editing complex protein MP44

+
Macromolecule #2: KREPB7

MacromoleculeName: KREPB7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 47.25309 KDa
SequenceString: MFQKTLRRLQ QQASQNPPVG SANIPSPYAT EGGHVPIWSI VNGFVQKRNW VFRNPEWCDL CKEPVALWVN HHGRKDHALM DMHYTQMME YPRRWNPEEV LVAFFDELQL PVETYQRSYT CYERAHRNEL YSMLVELEEA KMLYFGEPRN TYLHRMQGGL R GMDHQGAL ...String:
MFQKTLRRLQ QQASQNPPVG SANIPSPYAT EGGHVPIWSI VNGFVQKRNW VFRNPEWCDL CKEPVALWVN HHGRKDHALM DMHYTQMME YPRRWNPEEV LVAFFDELQL PVETYQRSYT CYERAHRNEL YSMLVELEEA KMLYFGEPRN TYLHRMQGGL R GMDHQGAL VLHRYILGPF MRLYPNAHIQ DFSNLVDFVT CAYNMETVYD LCGFYTLDKV ALKADYKPSS PAALGLGGIA VH SSPSHGF VQNAAESQQQ SRRASSTAST GSRSAADMDE EAFSRKAVFV RQLLGQLRWL TLPCEEHPAG CKFPQHLMLL GEI CLKYLV VEIIAARLCE YMVRVEPVWR DHGYERVKLN VDKIMKQGRD ILPEPIKYFY RPMSPNMDDL YSTKVGVLDE ALEK AAVTQ SLSKGV

UniProtKB: KREPB7

+
Macromolecule #3: RNA editing complex protein MP61

MacromoleculeName: RNA editing complex protein MP61 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427
Molecular weightTheoretical: 60.867977 KDa
SequenceString: MERGGRCLFR RWSTRALPSV SHTLRCRGTI SNSGGEGNDP IAEPRRVRLV PSAPHGNNSS ELFSVGVDPR SHTCDPDDPY SHIQIYRKD MVADAGGRAF QLSVDVPLKK FVDLFSDFDG KRCKLCNESY MQWHSHSSVI PHSGREALML EMVRAYCGLP E DIAKMWWH ...String:
MERGGRCLFR RWSTRALPSV SHTLRCRGTI SNSGGEGNDP IAEPRRVRLV PSAPHGNNSS ELFSVGVDPR SHTCDPDDPY SHIQIYRKD MVADAGGRAF QLSVDVPLKK FVDLFSDFDG KRCKLCNESY MQWHSHSSVI PHSGREALML EMVRAYCGLP E DIAKMWWH RLNTSPAFNR IPKLSHDNSH TRKRRLQYLL KFLKDRDVIR DTFNVHNSSG AAGRSWEFER LEWIGDNVVK YV FNDRFNV IFPVREGGIR GRLGYAQFMI DGNDGLARAY DYLELQKLTL SDRVVSKFKS DVVETLFGEL QLYIWSSETD AGT TCYPLP FTGEMFSLRA LVWHVMEELA HVMFMYHVEH ALAAIQRVVR ENQLQFIRAD PALRGHADLQ SELANTVYAK KAAS GPSKL TSTKVSPGAR FRDGGASFYH EASNYDGFKR VCTLGGLLPR PFSPRELTST TSFLPHLQED SAMTRRVPVD WTRKL FDDC TGNATKKPGA ANFVPWQAVT PQPRSRCSAE EAGRSTSRLG IPELKDALLV AELV

UniProtKB: RNA editing complex protein MP61

+
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

+
Macromolecule #5: MP18 RNA editing complex protein, putative

MacromoleculeName: MP18 RNA editing complex protein, putative / type: protein_or_peptide / ID: 5 / Number of copies: 3 / 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

+
Macromolecule #6: RNA-editing complex protein MP42

MacromoleculeName: RNA-editing complex protein MP42 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / 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

+
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

+
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

+
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

+
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

+
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: 24.825674 KDa
SequenceString:
GCGCUGAUGG UCUAGGUGGU UAUGACGUCG CUUUAACACG GCGAAGGUCU CGGGUUCGAG UCCCGAUCGG CGUACCA

+
Macromolecule #12: ZINC ION

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

+
Macromolecule #13: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 13 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #14: water

MacromoleculeName: water / type: ligand / ID: 14 / Number of copies: 199 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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: 300 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsFrom T. brucei mitochondrial T2 isolate

-
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

-
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

+
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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 496750
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

-
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-9z0h:
Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2)

+
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