[English] 日本語
Yorodumi- PDB-8any: Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-sit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8any | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | RIBOSOME / mitochondrial translation / mRNA delivery | ||||||||||||||||||
Function / homology | Function and homology information 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 translational elongation ...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 translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / 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 / anatomical structure morphogenesis / mRNA transport / 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 / endonuclease activity / nuclear membrane / cytosolic small ribosomal subunit / 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 / synapse / ubiquitin protein ligase binding / 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 | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å | ||||||||||||||||||
Authors | Singh, V. / Itoh, Y. / Amunts, A. | ||||||||||||||||||
Funding support | Sweden, European Union, 5items
| ||||||||||||||||||
Citation | Journal: To Be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8any.cif.gz | 7.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8any.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8any.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8any_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8any_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8any_validation.xml.gz | 356.6 KB | Display | |
Data in CIF | 8any_validation.cif.gz | 658.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/8any ftp://data.pdbj.org/pub/pdb/validation_reports/an/8any | HTTPS FTP |
-Related structure data
Related structure data | 15544MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 7 types, 7 molecules AAAwAxAyABAz
#1: RNA chain | Mass: 306218.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: GenBank: 1858621102 |
---|---|
#30: RNA chain | Mass: 21627.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#31: RNA chain | Mass: 22354.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#32: RNA chain | Mass: 22369.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#33: RNA chain | Mass: 500727.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#34: RNA chain | Mass: 22989.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#91: RNA chain | Mass: 13286.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
+28S ribosomal protein ... , 27 types, 27 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAZA0A1AY
-Protein , 9 types, 9 molecules A2A3bopqA5A4A6
#28: Protein | Mass: 13540.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2 |
---|---|
#29: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8 |
#67: Protein | Mass: 23352.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983 |
#79: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#80: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#81: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#88: Protein | Mass: 158098.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P42704 |
#89: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
#90: Protein | Mass: 12371.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9GZT3 |
+39S ribosomal protein ... , 48 types, 53 molecules DEFIJKLMNOPQRSTUVWXYZ012345678...
-Non-polymers , 12 types, 7197 molecules
#92: Chemical | ChemComp-NAD / | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#93: Chemical | ChemComp-SPM / | ||||||||||||||||||
#94: Chemical | ChemComp-SPD / #95: Chemical | ChemComp-MG / #96: Chemical | ChemComp-K / #97: Chemical | #98: Chemical | #99: Chemical | ChemComp-ATP / | #100: Chemical | ChemComp-GDP / | #101: Chemical | ChemComp-PUT / | #102: Chemical | ChemComp-VAL / | #103: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site Type: RIBOSOME / Entity ID: #1-#33, #35-#66, #68-#91 / Source: NATURAL |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82522 / Symmetry type: POINT |