+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23096 | |||||||||
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Title | Cryo-EM structure of the human 55S mitoribosome-RRFmt complex. | |||||||||
Map data | Cryo-EM structure of the human 55S mitoribosome-RRFmt complex. | |||||||||
Sample |
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Function / homology | Function and homology information mitochondrial ribosome binding / ribosome disassembly / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation ...mitochondrial ribosome binding / ribosome disassembly / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / small ribosomal subunit rRNA binding / fibrillar center / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / endonuclease activity / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / synapse / apoptotic process / GTP binding / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Koripella R / Agrawal EK / Deep A / Agrawal RK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance. Authors: Ravi Kiran Koripella / Ayush Deep / Ekansh K Agrawal / Pooja Keshavan / Nilesh K Banavali / Rajendra K Agrawal / Abstract: Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we ...Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRF) and a recycling-specific homolog of elongation factor G (EF-G2). These structures clarify an unusual role of a mitochondria-specific segment of RRF, identify the structural distinctions that confer functional specificity to EF-G2, and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2 is markedly different from that of mitochondrial elongation factor EF-G1, suggesting that the two human EF-Gs have evolved diversely to negate the effect of a bacterial antibiotic. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23096.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-23096-v30.xml emd-23096.xml | 95.3 KB 95.3 KB | Display Display | EMDB header |
Images | emd_23096.png | 158 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23096 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23096 | HTTPS FTP |
-Related structure data
Related structure data | 7l08MC 7l20C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10703 (Title: Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance Data size: 2.3 TB Data #1: Aligned single-frame particles of human mitochondrial 55S-EF-Gmt complex [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23096.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the human 55S mitoribosome-RRFmt complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Human mitochondrial ribosome-EF-G1 complex
+Supramolecule #1: Human mitochondrial ribosome-EF-G1 complex
+Macromolecule #1: 12S rRNA
+Macromolecule #32: 16S RRNA
+Macromolecule #33: tRNAVAL
+Macromolecule #2: 28S ribosomal protein S2, mitochondrial
+Macromolecule #3: 28S ribosomal protein S24, mitochondrial
+Macromolecule #4: 28S ribosomal protein S6, mitochondrial
+Macromolecule #5: 28S ribosomal protein S11, mitochondrial
+Macromolecule #6: 28S ribosomal protein S12, mitochondrial
+Macromolecule #7: 28S ribosomal protein S14, mitochondrial
+Macromolecule #8: 28S ribosomal protein S16, mitochondrial
+Macromolecule #9: 28S ribosomal protein S17, mitochondrial
+Macromolecule #10: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #11: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #12: 28S ribosomal protein S21, mitochondrial
+Macromolecule #13: 28S ribosomal protein S25, mitochondrial
+Macromolecule #14: 28S ribosomal protein S28, mitochondrial
+Macromolecule #15: 28S ribosomal protein S29, mitochondrial
+Macromolecule #16: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #17: 28S ribosomal protein S10, mitochondrial
+Macromolecule #18: 28S ribosomal protein S15, mitochondrial
+Macromolecule #19: 28S ribosomal protein S22, mitochondrial
+Macromolecule #20: 28S ribosomal protein S23, mitochondrial
+Macromolecule #21: 28S ribosomal protein S26, mitochondrial
+Macromolecule #22: 28S ribosomal protein S27, mitochondrial
+Macromolecule #23: 28S ribosomal protein S31, mitochondrial
+Macromolecule #24: 28S ribosomal protein S33, mitochondrial
+Macromolecule #25: 28S ribosomal protein S35, mitochondrial
+Macromolecule #26: 28S ribosomal protein S34, mitochondrial
+Macromolecule #27: Aurora kinase A-interacting protein
+Macromolecule #28: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #29: 28S ribosomal protein S5, mitochondrial
+Macromolecule #30: 28S ribosomal protein S7, mitochondrial
+Macromolecule #31: 28S ribosomal protein S9, mitochondrial
+Macromolecule #34: 39S ribosomal protein L2, mitochondrial
+Macromolecule #35: 39S ribosomal protein L4, mitochondrial
+Macromolecule #36: 39S ribosomal protein L9, mitochondrial
+Macromolecule #37: 39S ribosomal protein L13, mitochondrial
+Macromolecule #38: 39S ribosomal protein L14, mitochondrial
+Macromolecule #39: 39S ribosomal protein L15, mitochondrial
+Macromolecule #40: 39S ribosomal protein L17, mitochondrial
+Macromolecule #41: 39S ribosomal protein L20, mitochondrial
+Macromolecule #42: 39S ribosomal protein L21, mitochondrial
+Macromolecule #43: 39S ribosomal protein L22, mitochondrial
+Macromolecule #44: 39S ribosomal protein L27, mitochondrial
+Macromolecule #45: 39S ribosomal protein L28, mitochondrial
+Macromolecule #46: 39S ribosomal protein L47, mitochondrial
+Macromolecule #47: 39S ribosomal protein L30, mitochondrial
+Macromolecule #48: 39S ribosomal protein L32, mitochondrial
+Macromolecule #49: 39S ribosomal protein L33, mitochondrial
+Macromolecule #50: 39S ribosomal protein L34, mitochondrial
+Macromolecule #51: 39S ribosomal protein L35, mitochondrial
+Macromolecule #52: 39S ribosomal protein L36, mitochondrial
+Macromolecule #53: 39S ribosomal protein L40, mitochondrial
+Macromolecule #54: 39S ribosomal protein L43, mitochondrial
+Macromolecule #55: 39S ribosomal protein L46, mitochondrial
+Macromolecule #56: 39S ribosomal protein L49, mitochondrial
+Macromolecule #57: 39S ribosomal protein L51, mitochondrial
+Macromolecule #58: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribos...
+Macromolecule #59: 39S ribosomal protein L55, mitochondrial
+Macromolecule #60: Ribosomal protein 63, mitochondrial
+Macromolecule #61: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #62: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #63: 39S ribosomal protein L11, mitochondrial
+Macromolecule #64: 39S ribosomal protein L10, mitochondrial
+Macromolecule #65: 39S ribosomal protein L16, mitochondrial
+Macromolecule #66: Mitochondrial ribosomal protein L18, isoform CRA_b
+Macromolecule #67: 39S ribosomal protein L23, mitochondrial
+Macromolecule #68: 39S ribosomal protein L24, mitochondrial
+Macromolecule #69: 39S ribosomal protein L3, mitochondrial
+Macromolecule #70: 39S ribosomal protein L37, mitochondrial
+Macromolecule #71: 39S ribosomal protein L38, mitochondrial
+Macromolecule #72: 39S ribosomal protein L39, mitochondrial
+Macromolecule #73: 39S ribosomal protein L41, mitochondrial
+Macromolecule #74: 39S ribosomal protein L42, mitochondrial
+Macromolecule #75: 39S ribosomal protein L44, mitochondrial
+Macromolecule #76: 39S ribosomal protein L45, mitochondrial
+Macromolecule #77: 39S ribosomal protein L48, mitochondrial
+Macromolecule #78: 39S ribosomal protein L50, mitochondrial
+Macromolecule #79: 39S ribosomal protein L53, mitochondrial
+Macromolecule #80: 39S ribosomal protein L54, mitochondrial
+Macromolecule #81: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #82: 39S ribosomal protein S30, mitochondrial
+Macromolecule #83: 39S ribosomal protein L19, mitochondrial
+Macromolecule #84: P-site finger
+Macromolecule #85: 39S ribosomal protein L12, mitochondrial
+Macromolecule #86: Ribosome-recycling factor, mitochondrial
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: ZINC ION
+Macromolecule #89: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
Details | mitoribosome complex with mtEFG2 and mt RRF |
-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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 69.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER |
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Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93212 |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7l08: |