+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16593 | |||||||||
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Title | Cryo-EM map of RESC1-RESC2 bound to gRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RESC / RNA editing / cryo-EM structure / Trypanosoma brucei / RNA BINDING PROTEIN | |||||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Dolce LG / Kowalinski E | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Structural basis for guide RNA selection by the RESC1-RESC2 complex. Authors: Luciano G Dolce / Yevheniia Nesterenko / Leon Walther / Félix Weis / Eva Kowalinski / Abstract: Kinetoplastid parasites, such as trypanosomes or leishmania, rely on RNA-templated RNA editing to mature mitochondrial cryptic pre-mRNAs into functional protein-coding transcripts. Processive pan- ...Kinetoplastid parasites, such as trypanosomes or leishmania, rely on RNA-templated RNA editing to mature mitochondrial cryptic pre-mRNAs into functional protein-coding transcripts. Processive pan-editing of multiple editing blocks within a single transcript is dependent on the 20-subunit RNA editing substrate binding complex (RESC) that serves as a platform to orchestrate the interactions between pre-mRNA, guide RNAs (gRNAs), the catalytic RNA editing complex (RECC), and a set of RNA helicases. Due to the lack of molecular structures and biochemical studies with purified components, neither the spacio-temporal interplay of these factors nor the selection mechanism for the different RNA components is understood. Here we report the cryo-EM structure of Trypanosoma brucei RESC1-RESC2, a central hub module of the RESC complex. The structure reveals that RESC1 and RESC2 form an obligatory domain-swapped dimer. Although the tertiary structures of both subunits closely resemble each other, only RESC2 selectively binds 5'-triphosphate-nucleosides, a defining characteristic of gRNAs. We therefore propose RESC2 as the protective 5'-end binding site for gRNAs within the RESC complex. Overall, our structure provides a starting point for the study of the assembly and function of larger RNA-bound kinetoplast RNA editing modules and might aid in the design of anti-parasite drugs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16593.map.gz | 80.5 MB | EMDB map data format | |
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Header (meta data) | emd-16593-v30.xml emd-16593.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16593_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_16593.png | 56.3 KB | ||
Masks | emd_16593_msk_1.map | 103 MB | Mask map | |
Others | emd_16593_additional_1.map.gz emd_16593_additional_2.map.gz emd_16593_half_map_1.map.gz emd_16593_half_map_2.map.gz | 7.4 MB 91.3 MB 80.9 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16593 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16593 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16593.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16593_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Relion post process
File | emd_16593_additional_1.map | ||||||||||||
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Annotation | Relion post process | ||||||||||||
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Density Histograms |
-Additional map: deepEMhancer post process
File | emd_16593_additional_2.map | ||||||||||||
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Annotation | deepEMhancer post process | ||||||||||||
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-Half map: #1
File | emd_16593_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16593_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RESC1-RESC2-gRNA complex
Entire | Name: RESC1-RESC2-gRNA complex |
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Components |
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-Supramolecule #1: RESC1-RESC2-gRNA complex
Supramolecule | Name: RESC1-RESC2-gRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
Molecular weight | Theoretical: 118 KDa |
-Macromolecule #1: RESC1
Macromolecule | Name: RESC1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MKHHHHHHSA GLEVLFQGPD SMQNQGSVSQ GALNMRDQQA AAAENVTPER VWALWNEGNL FSLSLAQLQG FLSRCGVRTD PAAKKAAVVR QVEEYLHSKD TTVKGGGQGA ASPQQHQQHG QQGGYGRWNQ ASVMQPETLL DLSQAGFYEG AANMVPKAFQ LLVSDTAPDV ...String: MKHHHHHHSA GLEVLFQGPD SMQNQGSVSQ GALNMRDQQA AAAENVTPER VWALWNEGNL FSLSLAQLQG FLSRCGVRTD PAAKKAAVVR QVEEYLHSKD TTVKGGGQGA ASPQQHQQHG QQGGYGRWNQ ASVMQPETLL DLSQAGFYEG AANMVPKAFQ LLVSDTAPDV VVSRVNTTAF PGFPSNTECY TLGASEKDVA IRSRYSKVLQ WCCLNMSNLQ MDGELYVDFG KLLLKPSVMR KNRRIVSSYT LQQRLQVNHP YTWVPTLPES CLSKIQEQFL QPEGFAPIGK GVQLTYSGTI KRSKDQLHVD LDNKGKVLAV NSAWVNLQTA WCTHAKGPDV RLLLRSRPPI RRQDVELFAS TPIIKLADDD VADVLPPEHG QLVYLSEDET RLFERVSDRG VTITVREVKR QPLIILRDEE EDPRVEYSLS AHIPANAAKA TDVRAVGLTA FELAGRLAGL VAEDFVREYG CEAKL |
-Macromolecule #2: RESC2
Macromolecule | Name: RESC2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MQSFSAAAPA ASGDFSHITR NTVWGLWNEG NLFSLSVPEL AFFLQEHCRV ANVDPRAKKS ALVRQVEEIL SAEQQASATV PQEDNPHAIV VTDYDRAEDA LEEADEYGDW GAEPGFEDRR ELDFMELSPG RMGERYDPLS PRAFQLLHSE TATDVGIASI DPSKLPGQSK ...String: MQSFSAAAPA ASGDFSHITR NTVWGLWNEG NLFSLSVPEL AFFLQEHCRV ANVDPRAKKS ALVRQVEEIL SAEQQASATV PQEDNPHAIV VTDYDRAEDA LEEADEYGDW GAEPGFEDRR ELDFMELSPG RMGERYDPLS PRAFQLLHSE TATDVGIASI DPSKLPGQSK VKNALAAIHV APNDANKMRF RMAFEWCLMN IWNMNMPGEL NIGAGKALYY RSVAKQNRNV MPLWTVQKHL YAQHPYAWFA IASESNVAAM ESLAAALNMS IQQERTTSYK VTIRRMAEFF DCELNGQLKC TMMNKPWDRF FVSHYIRSKM PDLRYVVRAR HPIKKRIADA YLEADILRST RDSVQSVLSP ELGDVVYCCE RVVRKWAKKT ATGVTLQLVE TKRTPLIITK AGDEGERLEY EWIVPLPQQA ERIDIAALTD ELWEYGNKLA AALEEGMEEL MVHTMTAVSA Y |
-Macromolecule #3: gRNA gND7(506)
Macromolecule | Name: gRNA gND7(506) / type: rna / ID: 3 |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
Sequence | String: GGGAUAUAAA UACGAUGUAA AUAACCUGUA GUAUAGUUAG UGUAUAUAGU GAAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 62.9 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |