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- EMDB-21233: Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21233 | |||||||||
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Title | Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI) | |||||||||
![]() | ClassI 55S-EF-G1mt complex | |||||||||
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![]() | mitochondrial elongation factor-G1 / 55S ribosome / RIBOSOME | |||||||||
Function / homology | ![]() mitochondrial ribosome binding / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation ...mitochondrial ribosome binding / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / 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 / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / translation elongation factor activity / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / cell junction / large ribosomal subunit / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cytosolic large ribosomal subunit / cell population proliferation / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / nucleotide binding / synapse / positive regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
![]() | Sharma MR / Koripella RK | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Authors: Ravi Kiran Koripella / Manjuli R Sharma / Kalpana Bhargava / Partha P Datta / Prem S Kaushal / Pooja Keshavan / Linda L Spremulli / Nilesh K Banavali / Rajendra K Agrawal / ![]() ![]() Abstract: The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we ...The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1 in mitochondrial tRNA (tRNA) translocation. In particular, the mito-specific C-terminal extension in EF-G1 is directly involved in translocation of the acceptor arm of the A-site tRNA. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 105.5 KB 105.5 KB | Display Display | ![]() |
Images | ![]() | 249.7 KB | ||
Filedesc metadata | ![]() | 22.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vlzMC ![]() 6vmiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 753.5 Data #1: Aligned single-frame particles of human mitochondrial 55S-EF-Gmt complex [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ClassI 55S-EF-G1mt complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0961 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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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: 39S ribosomal protein L12, mitochondrial
+Macromolecule #85: P-site finger
+Macromolecule #86: Elongation factor G, mitochondrial
+Macromolecule #87: mRNA
+Macromolecule #88: E-tRNA
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: ZINC ION
+Macromolecule #91: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #92: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 69.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99804 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |