[English] 日本語
Yorodumi- EMDB-54639: Structure of human mitochondrial COX1-translating ribosome nascen... -
+
Open data
-
Basic information
| Entry | ![]() | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Structure of human mitochondrial COX1-translating ribosome nascent chain-OXA1L/MITRAC complex in open state (open COX1-mtRNC-OXA1L/MITRAC) | |||||||||||||||
Map data | ||||||||||||||||
Sample |
| |||||||||||||||
Keywords | mt55S / ribosome / micochondria / COX1 / membrane / translation | |||||||||||||||
| Function / homology | Function and homology informationmitochondrial protein quality control / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / Complex I biogenesis / negative regulation of ATP-dependent activity / mitochondrial transcription / rRNA import into mitochondrion / rescue of stalled mitochondrial ribosome ...mitochondrial protein quality control / negative regulation of oxidoreductase activity / mitochondrial ribosome binding / protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / Complex I biogenesis / negative regulation of ATP-dependent activity / mitochondrial transcription / rRNA import into mitochondrion / rescue of stalled mitochondrial ribosome / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / mitochondrial translation / ribosomal small subunit binding / positive regulation of proteolysis / mitochondrial respiratory chain complex I assembly / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / apoptotic signaling pathway / aerobic respiration / protein tetramerization / fibrillar center / cell population proliferation / mitochondrial membrane / regulation of translation / double-stranded RNA binding / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / negative regulation of translation / mitochondrial inner membrane / rRNA binding / ribosome / translation / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / apoptotic process / mRNA binding / GTPase activity / positive regulation of DNA-templated transcription / GTP binding / protein homodimerization activity / protein-containing complex / mitochondrion / : / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
| Biological species | Homo sapiens (human) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Schoendorf T / Petrychenko V / Kotan I / Cruz-Zaragoza LD / Dahal D / Wang C / Gal T / Dennerlein S / Kramer G / Fischer N / Rehling P | |||||||||||||||
| Funding support | European Union, Germany, 4 items
| |||||||||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2026Title: Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed. Authors: Thomas Schöndorf / Valentyn Petrychenko / Ilgin Kotan / Drishan Dahal / Natalia Napieraj / Luis Daniel Cruz-Zaragoza / Cong Wang / Oliver Urbach / Tanja Gall / Sven Dennerlein / Günter ...Authors: Thomas Schöndorf / Valentyn Petrychenko / Ilgin Kotan / Drishan Dahal / Natalia Napieraj / Luis Daniel Cruz-Zaragoza / Cong Wang / Oliver Urbach / Tanja Gall / Sven Dennerlein / Günter Kramer / Niels Fischer / Peter Rehling / ![]() Abstract: The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ...The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not sufficiently understood. Here, we applied ribosome profiling to assess translation dynamics in combination with cryo-electron microscopy analysis of a COX1 ribosome-nascent chain complex to visualize cotranslational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation pausing events. Thus, our findings reveal a link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane. | |||||||||||||||
| History |
|
-
Structure visualization
| Supplemental images |
|---|
-
Downloads & links
-EMDB archive
| Map data | emd_54639.map.gz | 122 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-54639-v30.xml emd-54639.xml | 117.8 KB 117.8 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_54639_fsc.xml | 14.1 KB | Display | FSC data file |
| Images | emd_54639.png | 108.7 KB | ||
| Masks | emd_54639_msk_1.map | 244.1 MB | Mask map | |
| Filedesc metadata | emd-54639.cif.gz | 23.9 KB | ||
| Others | emd_54639_half_map_1.map.gz emd_54639_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54639 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54639 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9s7dMC ![]() 9s7bC ![]() 9s7cC ![]() 9s7eC M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_54639.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
|
-Supplemental data
-Mask #1
| File | emd_54639_msk_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: #2
| File | emd_54639_half_map_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: #1
| File | emd_54639_half_map_2.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-
Sample components
+Entire : Human mitochondrial 55S ribosome complex with tRNAs and COX1 nasc...
+Supramolecule #1: Human mitochondrial 55S ribosome complex with tRNAs and COX1 nasc...
+Macromolecule #1: 16S mitochondrial rRNA
+Macromolecule #2: mitochondrial tRNAVal
+Macromolecule #25: 12S mitochondrial rRNA
+Macromolecule #85: mRNA (Visualization example)
+Macromolecule #86: A-site tRNA (Visualisation example)
+Macromolecule #87: P-site tRNA (Visualisation example)
+Macromolecule #3: Large ribosomal subunit protein uL2m
+Macromolecule #4: Large ribosomal subunit protein uL3m
+Macromolecule #5: Large ribosomal subunit protein uL4m
+Macromolecule #6: Large ribosomal subunit protein bL9m
+Macromolecule #7: Large ribosomal subunit protein uL10m
+Macromolecule #8: Large ribosomal subunit protein uL11m
+Macromolecule #9: Large ribosomal subunit protein uL13m
+Macromolecule #10: Large ribosomal subunit protein uL14m
+Macromolecule #11: Large ribosomal subunit protein uL15m
+Macromolecule #12: Large ribosomal subunit protein uL16m
+Macromolecule #13: Large ribosomal subunit protein bL17m
+Macromolecule #14: Large ribosomal subunit protein uL18m
+Macromolecule #15: Large ribosomal subunit protein bL19m
+Macromolecule #16: Large ribosomal subunit protein bL20m
+Macromolecule #17: Large ribosomal subunit protein bL21m
+Macromolecule #18: Large ribosomal subunit protein uL22m
+Macromolecule #19: Large ribosomal subunit protein uL23m
+Macromolecule #20: Large ribosomal subunit protein uL24m
+Macromolecule #21: Large ribosomal subunit protein bL27m
+Macromolecule #22: Large ribosomal subunit protein bL28m
+Macromolecule #23: Large ribosomal subunit protein uL29m
+Macromolecule #24: Large ribosomal subunit protein uL30m
+Macromolecule #26: Small ribosomal subunit protein uS2m
+Macromolecule #27: Small ribosomal subunit protein uS3m
+Macromolecule #28: Large ribosomal subunit protein bL32m
+Macromolecule #29: Large ribosomal subunit protein bL33m
+Macromolecule #30: Large ribosomal subunit protein bL34m
+Macromolecule #31: Large ribosomal subunit protein bL35m
+Macromolecule #32: Large ribosomal subunit protein bL36m
+Macromolecule #33: Large ribosomal subunit protein uL1m
+Macromolecule #34: Large ribosomal subunit protein bL12m
+Macromolecule #35: Large ribosomal subunit protein mL37
+Macromolecule #36: Large ribosomal subunit protein mL38
+Macromolecule #37: Large ribosomal subunit protein mL39
+Macromolecule #38: Large ribosomal subunit protein mL40
+Macromolecule #39: Large ribosomal subunit protein mL41
+Macromolecule #40: Large ribosomal subunit protein mL42
+Macromolecule #41: Large ribosomal subunit protein mL43
+Macromolecule #42: Large ribosomal subunit protein mL44
+Macromolecule #43: Large ribosomal subunit protein mL46
+Macromolecule #44: Large ribosomal subunit protein mL48
+Macromolecule #45: Large ribosomal subunit protein mL49
+Macromolecule #46: Large ribosomal subunit protein mL50
+Macromolecule #47: Large ribosomal subunit protein mL51
+Macromolecule #48: Large ribosomal subunit protein mL52
+Macromolecule #49: Large ribosomal subunit protein mL53
+Macromolecule #50: Large ribosomal subunit protein mL54
+Macromolecule #51: Large ribosomal subunit protein mL55
+Macromolecule #52: Large ribosomal subunit protein mL63
+Macromolecule #53: Large ribosomal subunit protein mL62
+Macromolecule #54: Large ribosomal subunit protein mL64
+Macromolecule #55: Large ribosomal subunit protein mL66
+Macromolecule #56: Large ribosomal subunit protein mL65
+Macromolecule #57: Small ribosomal subunit protein uS5m
+Macromolecule #58: Small ribosomal subunit protein bS6m
+Macromolecule #59: Small ribosomal subunit protein uS7m
+Macromolecule #60: Small ribosomal subunit protein uS9m
+Macromolecule #61: Small ribosomal subunit protein uS10m
+Macromolecule #62: Small ribosomal subunit protein uS11m
+Macromolecule #63: Small ribosomal subunit protein uS12m
+Macromolecule #64: Small ribosomal subunit protein uS14m
+Macromolecule #65: Small ribosomal subunit protein uS15m
+Macromolecule #66: Small ribosomal subunit protein bS16m
+Macromolecule #67: Small ribosomal subunit protein uS17m
+Macromolecule #68: Small ribosomal subunit protein mS40
+Macromolecule #69: Small ribosomal subunit protein bS18m
+Macromolecule #70: Small ribosomal subunit protein bS21m
+Macromolecule #71: Small ribosomal subunit protein mS22
+Macromolecule #72: Small ribosomal subunit protein mS23
+Macromolecule #73: Small ribosomal subunit protein mS25
+Macromolecule #74: Small ribosomal subunit protein mS26
+Macromolecule #75: Small ribosomal subunit protein mS27
+Macromolecule #76: Small ribosomal subunit protein bS1m
+Macromolecule #77: Small ribosomal subunit protein mS29
+Macromolecule #78: Small ribosomal subunit protein mS31
+Macromolecule #79: Small ribosomal subunit protein mS33
+Macromolecule #80: Small ribosomal subunit protein mS34
+Macromolecule #81: Small ribosomal subunit protein mS35
+Macromolecule #82: Small ribosomal subunit protein mS37
+Macromolecule #83: Small ribosomal subunit protein bS22, mitochondrial
+Macromolecule #84: Small ribosomal subunit protein mS39
+Macromolecule #88: COX1 nascent chain
+Macromolecule #89: Large ribosomal subunit protein mL45
+Macromolecule #90: Mitochondrial inner membrane protein OXA1L
+Macromolecule #91: POTASSIUM ION
+Macromolecule #92: MAGNESIUM ION
+Macromolecule #93: VALINE
+Macromolecule #94: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #95: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #96: ZINC ION
+Macromolecule #97: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #98: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Buffer | pH: 7.4 / Details: Methods part of the manuscript |
|---|---|
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing. |
-
Electron microscopy
| Microscope | TFS KRIOS |
|---|---|
| Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 54447 / Average electron dose: 35.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
| Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
|---|---|
| Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: RSCC |
| Output model | ![]() PDB-9s7d: |
Movie
Controller
About Yorodumi



Keywords
Homo sapiens (human)
Authors
Germany, 4 items
Citation




























Z (Sec.)
Y (Row.)
X (Col.)

















































FIELD EMISSION GUN



