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- EMDB-15544: Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-sit... -
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Open data
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Basic information
Entry | ![]() | ||||||||||||||||||
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Title | Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA | ||||||||||||||||||
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![]() | mitochondrial translation / mRNA delivery / RIBOSOME | ||||||||||||||||||
Function / homology | ![]() negative regulation of mitochondrial RNA catabolic process / : / mitochondrial RNA catabolic process / regulation of mitochondrial translation / flagellated sperm motility / mitochondrial ribosome binding / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial transcription / mitochondrial ribosome assembly ...negative regulation of mitochondrial RNA catabolic process / : / mitochondrial RNA catabolic process / regulation of mitochondrial translation / flagellated sperm motility / mitochondrial ribosome binding / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / nuclear outer membrane / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrion transport along microtubule / nuclear inner membrane / mitochondrial ribosome / mitochondrial translation / beta-tubulin binding / mitochondrial nucleoid / positive regulation of proteolysis / ribosomal small subunit binding / spermatid development / single fertilization / sperm flagellum / mRNA transport / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / acrosomal vesicle / condensed nuclear chromosome / cellular response to leukemia inhibitory factor / mRNA 3'-UTR binding / TP53 Regulates Metabolic Genes / apoptotic signaling pathway / Cytoprotection by HMOX1 / fibrillar center / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / single-stranded DNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / microtubule binding / nuclear membrane / cytosolic small ribosomal subunit / endonuclease activity / microtubule / cell population proliferation / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / cytoskeleton / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / nucleolus / GTP binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / mitochondrion / RNA binding / extracellular space / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | ||||||||||||||||||
![]() | Singh V / Itoh Y / Amunts A | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome Authors: Singh V / Conor J / Itoh Y / Soto T / Fontanesi F / Couvillian M / Huynen M / Churchman S / Barrientos A / Amunts A | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 571.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 118.1 KB 118.1 KB | Display Display | ![]() |
Images | ![]() | 104.2 KB | ||
Filedesc metadata | ![]() | 24.1 KB | ||
Others | ![]() ![]() | 559.4 MB 558.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8anyMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_15544_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: consensus unsharpened
File | emd_15544_additional_2.map | ||||||||||||
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Annotation | consensus unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...
+Supramolecule #1: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...
+Macromolecule #1: 12S mitochondrial rRNA
+Macromolecule #30: A/A-tRNA
+Macromolecule #31: P/P-tRNA
+Macromolecule #32: E/E-tRNA
+Macromolecule #33: 16S mitochondrial rRNA
+Macromolecule #34: mitochondrial tRNAVal
+Macromolecule #91: mRNA
+Macromolecule #2: 28S ribosomal protein S2, mitochondrial
+Macromolecule #3: 28S ribosomal protein S24, mitochondrial
+Macromolecule #4: 28S ribosomal protein S5, mitochondrial
+Macromolecule #5: 28S ribosomal protein S6, mitochondrial
+Macromolecule #6: 28S ribosomal protein S7, mitochondrial
+Macromolecule #7: 28S ribosomal protein S9, mitochondrial
+Macromolecule #8: 28S ribosomal protein S10, mitochondrial
+Macromolecule #9: 28S ribosomal protein S11, mitochondrial
+Macromolecule #10: 28S ribosomal protein S12, mitochondrial
+Macromolecule #11: 28S ribosomal protein S14, mitochondrial
+Macromolecule #12: 28S ribosomal protein S15, mitochondrial
+Macromolecule #13: 28S ribosomal protein S16, mitochondrial
+Macromolecule #14: 28S ribosomal protein S17, mitochondrial
+Macromolecule #15: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #16: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #17: 28S ribosomal protein S21, mitochondrial
+Macromolecule #18: 28S ribosomal protein S22, mitochondrial
+Macromolecule #19: 28S ribosomal protein S23, mitochondrial
+Macromolecule #20: 28S ribosomal protein S25, mitochondrial
+Macromolecule #21: 28S ribosomal protein S26, mitochondrial
+Macromolecule #22: 28S ribosomal protein S27, mitochondrial
+Macromolecule #23: 28S ribosomal protein S28, mitochondrial
+Macromolecule #24: 28S ribosomal protein S29, mitochondrial
+Macromolecule #25: 28S ribosomal protein S33, mitochondrial
+Macromolecule #26: 28S ribosomal protein S34, mitochondrial
+Macromolecule #27: 28S ribosomal protein S35, mitochondrial
+Macromolecule #28: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #29: Aurora kinase A-interacting protein
+Macromolecule #35: 39S ribosomal protein L2, mitochondrial
+Macromolecule #36: 39S ribosomal protein L3, mitochondrial
+Macromolecule #37: 39S ribosomal protein L4, mitochondrial
+Macromolecule #38: 39S ribosomal protein L10, mitochondrial
+Macromolecule #39: 39S ribosomal protein L11, mitochondrial
+Macromolecule #40: 39S ribosomal protein L13, mitochondrial
+Macromolecule #41: 39S ribosomal protein L14, mitochondrial
+Macromolecule #42: 39S ribosomal protein L15, mitochondrial
+Macromolecule #43: 39S ribosomal protein L16, mitochondrial
+Macromolecule #44: 39S ribosomal protein L17, mitochondrial
+Macromolecule #45: 39S ribosomal protein L18, mitochondrial
+Macromolecule #46: 39S ribosomal protein L19, mitochondrial
+Macromolecule #47: 39S ribosomal protein L20, mitochondrial
+Macromolecule #48: 39S ribosomal protein L21, mitochondrial
+Macromolecule #49: 39S ribosomal protein L22, mitochondrial
+Macromolecule #50: 39S ribosomal protein L23, mitochondrial
+Macromolecule #51: 39S ribosomal protein L24, mitochondrial
+Macromolecule #52: 39S ribosomal protein L27, mitochondrial
+Macromolecule #53: 39S ribosomal protein L28, mitochondrial
+Macromolecule #54: 39S ribosomal protein L47, mitochondrial
+Macromolecule #55: 39S ribosomal protein L30, mitochondrial
+Macromolecule #56: 39S ribosomal protein L32, mitochondrial
+Macromolecule #57: 39S ribosomal protein L33, mitochondrial
+Macromolecule #58: 39S ribosomal protein L34, mitochondrial
+Macromolecule #59: 39S ribosomal protein L35, mitochondrial
+Macromolecule #60: 39S ribosomal protein L36, mitochondrial
+Macromolecule #61: 39S ribosomal protein L37, mitochondrial
+Macromolecule #62: 39S ribosomal protein L38, mitochondrial
+Macromolecule #63: 39S ribosomal protein L39, mitochondrial
+Macromolecule #64: 39S ribosomal protein L40, mitochondrial
+Macromolecule #65: 39S ribosomal protein L41, mitochondrial
+Macromolecule #66: 39S ribosomal protein L42, mitochondrial
+Macromolecule #67: Large ribosomal subunit protein mL43
+Macromolecule #68: 39S ribosomal protein L44, mitochondrial
+Macromolecule #69: 39S ribosomal protein L45, mitochondrial
+Macromolecule #70: 39S ribosomal protein L46, mitochondrial
+Macromolecule #71: 39S ribosomal protein L48, mitochondrial
+Macromolecule #72: 39S ribosomal protein L49, mitochondrial
+Macromolecule #73: 39S ribosomal protein L50, mitochondrial
+Macromolecule #74: 39S ribosomal protein L51, mitochondrial
+Macromolecule #75: 39S ribosomal protein L52, mitochondrial
+Macromolecule #76: 39S ribosomal protein L53, mitochondrial
+Macromolecule #77: 39S ribosomal protein L54, mitochondrial
+Macromolecule #78: 39S ribosomal protein L55, mitochondrial
+Macromolecule #79: Ribosomal protein 63, mitochondrial
+Macromolecule #80: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #81: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #82: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #83: 39S ribosomal protein S30, mitochondrial
+Macromolecule #84: 39S ribosomal protein L12, mitochondrial
+Macromolecule #85: 39S ribosomal protein L9, mitochondrial
+Macromolecule #86: 39S ribosomal protein L1, mitochondrial
+Macromolecule #87: 28S ribosomal protein S31, mitochondrial
+Macromolecule #88: Leucine-rich PPR motif-containing protein, mitochondrial
+Macromolecule #89: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #90: SRA stem-loop-interacting RNA-binding protein, mitochondrial
+Macromolecule #92: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #93: SPERMINE
+Macromolecule #94: SPERMIDINE
+Macromolecule #95: MAGNESIUM ION
+Macromolecule #96: POTASSIUM ION
+Macromolecule #97: ZINC ION
+Macromolecule #98: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #99: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #100: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #101: 1,4-DIAMINOBUTANE
+Macromolecule #102: VALINE
+Macromolecule #103: water
-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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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82522 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |