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- EMDB-29308: Cryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing -

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Basic information

Entry
Database: EMDB / ID: EMD-29308
TitleCryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing
Map data
Sample
  • Complex: RESC5-tagged isolate with RNase treatment
    • RNA: mRNA
    • RNA: gRNA
    • Protein or peptide: Mitochondrial RNA binding protein
    • Protein or peptide: RAP domain-containing protein
    • Protein or peptide: RxLR effector protein
    • Protein or peptide: Mitochondrial RNA binding complex 1 subunit
    • Protein or peptide: RAP domain-containing protein
    • Protein or peptide: Phytanoyl-CoA dioxygenase family protein
KeywordsHEAT repeat / trypanosoma / RNA editing substrate binding complex / gRNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / mitochondrial mRNA editing complex / ribonucleoprotein granule / mitochondrial RNA processing / RNA metabolic process / kinetoplast / cytidine to uridine editing ...regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / mitochondrial mRNA editing complex / ribonucleoprotein granule / mitochondrial RNA processing / RNA metabolic process / kinetoplast / cytidine to uridine editing / 2-oxoglutarate-dependent dioxygenase activity / mRNA stabilization / post-transcriptional regulation of gene expression / RNA processing / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
: / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Armadillo-type fold
Similarity search - Domain/homology
Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding protein / Mitochondrial RNA binding complex 1 subunit / Phytanoyl-CoA dioxygenase / Mitochondrial RNA binding complex 1 subunit / Guide RNA binding protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu S / Wang H / Li X / Zhang F / Lee JKJ / Li Z / Yu C / Zhao X / Hu JJ / Suematsu T ...Liu S / Wang H / Li X / Zhang F / Lee JKJ / Li Z / Yu C / Zhao X / Hu JJ / Suematsu T / Alvarez-Cabrera AL / Liu Q / Zhang L / Huang L / Aphasizheva I / Aphasizhev R / Zhou ZH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI101057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: Science / Year: 2023
Title: Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing.
Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / ...Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial ...In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.
History
DepositionDec 27, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29308.png

Downloads & links

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Map

FileDownload / File: emd_29308.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.872 Å		1.06 Å/pix.
x 256 pix.
= 271.872 Å		1.06 Å/pix.
x 256 pix.
= 271.872 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.12132331 - 0.22136196
Average (Standard dev.)0.00021913073 (±0.006462722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.872 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29308_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29308_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : RESC5-tagged isolate with RNase treatment

EntireName: RESC5-tagged isolate with RNase treatment
Components
  • Complex: RESC5-tagged isolate with RNase treatment
    • RNA: mRNA
    • RNA: gRNA
    • Protein or peptide: Mitochondrial RNA binding protein
    • Protein or peptide: RAP domain-containing protein
    • Protein or peptide: RxLR effector protein
    • Protein or peptide: Mitochondrial RNA binding complex 1 subunit
    • Protein or peptide: RAP domain-containing protein
    • Protein or peptide: Phytanoyl-CoA dioxygenase family protein

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Supramolecule #1: RESC5-tagged isolate with RNase treatment

SupramoleculeName: RESC5-tagged isolate with RNase treatment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: CTS-tagged RESC5 purified from RNase-treated mitochondrial extract by tandem affinity procedure
Source (natural)Organism: Trypanosoma brucei (eukaryote)

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Macromolecule #1: mRNA

MacromoleculeName: mRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 5.507382 KDa
SequenceString:
UAAUAGAAUA AGAUAAG

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Macromolecule #2: gRNA

MacromoleculeName: gRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 4.968896 KDa
SequenceString:
UUUUUUUAAA UAAUUU

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Macromolecule #3: Mitochondrial RNA binding protein

MacromoleculeName: Mitochondrial RNA binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 34.727539 KDa
SequenceString: MLRHTSRNNA LHAFVRSPHY RTIPSAGPNG IVVNRDMLVH QFRDFYKTLQ HCSLVDKVHL MSERPSVEAL RVADQMVSIG ATFLEMPLT GMEHRATEFM ESMRYVRGAG GPSTLASYLQ DTENCRCNSG DVVCLPNGIA VGHGPRTNAV AHTTLKQLFE V KDDQFSFD ...String:
MLRHTSRNNA LHAFVRSPHY RTIPSAGPNG IVVNRDMLVH QFRDFYKTLQ HCSLVDKVHL MSERPSVEAL RVADQMVSIG ATFLEMPLT GMEHRATEFM ESMRYVRGAG GPSTLASYLQ DTENCRCNSG DVVCLPNGIA VGHGPRTNAV AHTTLKQLFE V KDDQFSFD VFTLEQEGDA PPLGDYFGFA GSNVLLTWKD EHGLLAVDQY QQKQPHTEMN VVYLEPGCHF LSFYGVDHTI DV LVQKGYE RSMDSIAAAG LNPIPVQWSE MDKLGISMRA AVLPLKFFKA NVGGMLSRNK SRGARWQTHQ LQK

UniProtKB: Mitochondrial RNA binding protein

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Macromolecule #4: RAP domain-containing protein

MacromoleculeName: RAP domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 57.823484 KDa
SequenceString: MRSALRRCIL RHQGCLRMKQ SLSAFPTVVT GMTRHQGNSL IGTTHGAELS LAGDPQSVSH LSARNIATEA LQMKKLHQER GGNPMLAQQ ARRVLFATSI AGQNLDARSV ALLLNTAVYF GMESDAKLVR ECIDYCLKND KLITVDVLPI VVTACATLKS R DAREVIEM ...String:
MRSALRRCIL RHQGCLRMKQ SLSAFPTVVT GMTRHQGNSL IGTTHGAELS LAGDPQSVSH LSARNIATEA LQMKKLHQER GGNPMLAQQ ARRVLFATSI AGQNLDARSV ALLLNTAVYF GMESDAKLVR ECIDYCLKND KLITVDVLPI VVTACATLKS R DAREVIEM QAQKAARNAK FLDAKDVTNI ISAFSKTGIN HEKLFAFLSR RVQTLARVGE FEAAHLVILA NAFSRLRYRD KF LFGAIAR RAMSLRERVT VNELVPLIVA FSKIGLKDPK LSKRFATKAM EYVDQMNAEQ VASMFMAFAY FGIRYDQLFG VLT NRAVEL IDEFNAQYIS TTLNAFQRIG INNPELFDNL AERALAVVQD HDARDISKTV TALAHFGLKD EELFKRLASH AASI ADQFD AMGLVNTAHA FARTNFLQQD MAVALSERSV YVCRLLDAGE TRRLLWALAK FQVRDPKILT PVFNRCLALH YDFFA DPTG SEEIEEIFDF YGPNFCPPLY QLYISRGSTP QA

UniProtKB: Guide RNA binding protein

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Macromolecule #5: RxLR effector protein

MacromoleculeName: RxLR effector protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 18.669676 KDa
SequenceString:
MRSSRGILFL SGAFAIRGMS AYHSYQRLDT VSHTSKVYSL QMQRQTVHFT PITRLGVEAT ANPTTATNAT GQTGDGDGAT ALDVAMRVN KLKRLHQTGG GPSGKKQVEL DAWRDLNNLT EAQINSAEGK AVSLLLNSWA YFAKYWEKGA EGPSASLSEV T PSNDSSSA GEHGTQ

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #6: Mitochondrial RNA binding complex 1 subunit

MacromoleculeName: Mitochondrial RNA binding complex 1 subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 61.109809 KDa
SequenceString: MLNVLSSTAS AALATVVVAR PSALHLIFER CKLNLVEFTA QDVYQICTTA YNMDTLGMLQ DPDFMRGLHD AFRRSDQTVI SPFQANLIA DTFRKVGINS MPKEVSVPEE DAISPESLIL VLRNMNITKQ RDERKINEVL KLMFPILDEF SPTQLSLTVT E LARLKSTN ...String:
MLNVLSSTAS AALATVVVAR PSALHLIFER CKLNLVEFTA QDVYQICTTA YNMDTLGMLQ DPDFMRGLHD AFRRSDQTVI SPFQANLIA DTFRKVGINS MPKEVSVPEE DAISPESLIL VLRNMNITKQ RDERKINEVL KLMFPILDEF SPTQLSLTVT E LARLKSTN ADFVGKLAKR IMEYNDDLSA LDISSAAVSL AYCPGISHNI LYRMMQIVEE RMGEFQPEDY INVLHALNTL GP KFVNTFR KIVECGLQHV ENMDAVTLTN YMVCFSTMDY KQREHIDIYA DALVEVATDL SEKDLVMAFI ALQRLRLLSD TMF GTMASC VIRYAAKMDP RNIAPIMDIC STVPHASDHL MKVLMDRAVE CTRILTANQL GDILDILGLY PPAREHPLVQ LFGK QARLR LDLMGPDALA NATRGLANLG YADPEYYAQA AETGFRYGFK DWTLLEPMLM GLSITGQCPP TMVRVLGSHI APMAR SMSL MEIERANRYL RRLGCEDDFV YKAMASRVLQ FVKEVTPEMP EDLQVLLQRG AVEPGAAPGV M

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #7: RAP domain-containing protein

MacromoleculeName: RAP domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 60.563676 KDa
SequenceString: MRRRVVLCCQ DVGSLLSSKH SVHSGIGYHE RVFSRNLLYR RYPVVTVLPK AGFTVLDTKR WIASSGPPVT GSPLSPVTNP SLNVGTGGG EAVAMEGPLP VSYSPGSGVN GSLPVTSTAI TAHCDVLSEC VAKADELAVQ LKAQNALSAS AEILTQEGME E FVEELKTS ...String:
MRRRVVLCCQ DVGSLLSSKH SVHSGIGYHE RVFSRNLLYR RYPVVTVLPK AGFTVLDTKR WIASSGPPVT GSPLSPVTNP SLNVGTGGG EAVAMEGPLP VSYSPGSGVN GSLPVTSTAI TAHCDVLSEC VAKADELAVQ LKAQNALSAS AEILTQEGME E FVEELKTS ATNEMTALVK QMQTTPLLQR AGMHELRRTL YYTTSLKERD WLEEKQYTAA MRMLTVEVLR RDGDGVLSAD DV LYVTTHV VTANFYNRHL WNRMEKSLLK FSNYENIDMS SVKAFSTRLF KTRRGCAKET LDIRRKVLLA MSRRVGVLAN DFD LPSLLG VLQCYTVHDL TPFHLEPLAI RATNHVGDFT PHECATLAHV LRKWRTMRLE VCERLVERIC TSDQLTHHMA NAAM IAIRT CFNQVSDGGR NAMNAEPTRQ KLRAMGEQIG CRLDEVEYPA LPVILSILDV VVTLKIYVPK KCLQVIFSQA NDMVA IVME QKDDLVDPKT GKRVRPITAE EGRQLQALLS HYGNDLAPEL SQRMKEAFRE GVLPDEASL

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #8: Phytanoyl-CoA dioxygenase family protein

MacromoleculeName: Phytanoyl-CoA dioxygenase family protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 41.293148 KDa
SequenceString: MRSGRKLGCF TNRLRLPFFS PCSQITALTA SHRCKSYVLK FLRGQLPEDL KDVNGALGCL YGTLPDVDEF GQFVISPDVV NSFHQFGYV KMPIPVLDHQ QIDKLADEVN ELANNVEHHP KTERLYATSL ADLTGGPLFF CQGQWRAAWG MHDLIYLPTI T VAASQILN ...String:
MRSGRKLGCF TNRLRLPFFS PCSQITALTA SHRCKSYVLK FLRGQLPEDL KDVNGALGCL YGTLPDVDEF GQFVISPDVV NSFHQFGYV KMPIPVLDHQ QIDKLADEVN ELANNVEHHP KTERLYATSL ADLTGGPLFF CQGQWRAAWG MHDLIYLPTI T VAASQILN NSLVRLWYDE VFMKAARTGP CVPWQQNYAR WQHTKPVNHV TVMIALDTMN KDRGAPCLVP GSHRWREGGL LP PVSYDPT KDEAHQLNTI WEIINEEEGE MLMDTPPVTV DLRRGEALLI HPLTLFATHG NRSLDAVRCC FIHYMGEKTY AVQ NGPLLP HTTKFQADAM IQGPFYPVVF DPAMTEELTM LPTAPSEEEA

UniProtKB: Phytanoyl-CoA dioxygenase

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 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: 1.5 µm
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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 414524
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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