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Yorodumi- PDB-7oi6: Cryo-EM structure of late human 39S mitoribosome assembly interme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oi6 | |||||||||
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Title | Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1 | |||||||||
Components |
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Keywords | RIBOSOME / 39S mitoribosome / ribosome biogenesis | |||||||||
Function / homology | Function and homology information rRNA (guanosine-2'-O-)-methyltransferase activity / ribonucleoprotein granule / rRNA modification in the mitochondrion / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Protein lipoylation / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation ...rRNA (guanosine-2'-O-)-methyltransferase activity / ribonucleoprotein granule / rRNA modification in the mitochondrion / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Protein lipoylation / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / mitochondrial nucleoid / ribosomal large subunit binding / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / ribosome biogenesis / chromosome / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cell cycle / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / RNA helicase activity / nuclear body / rRNA binding / negative regulation of translation / hydrolase activity / ribosome / RNA helicase / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / calcium ion binding / GTP binding / nucleolus / magnesium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Cheng, J. / Berninghausen, O. / Beckmann, R. | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: A distinct assembly pathway of the human 39S late pre-mitoribosome. Authors: Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Abstract: Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. ...Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oi6.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oi6.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7oi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oi6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7oi6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7oi6_validation.xml.gz | 194.7 KB | Display | |
Data in CIF | 7oi6_validation.cif.gz | 345 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/7oi6 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/7oi6 | HTTPS FTP |
-Related structure data
Related structure data | 12919MC 7oi7C 7oi8C 7oi9C 7oiaC 7oibC 7oicC 7oidC 7oieC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+39S ribosomal protein ... , 40 types, 40 molecules DEFHKLMNOQRSTUVXYZ02579abcdghi...
-Protein , 9 types, 10 molecules opquvwxyz1
#32: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
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#33: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#34: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#37: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3 |
#38: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#39: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
#41: Protein | Mass: 59666.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NUL7, RNA helicase |
#42: Protein | Mass: 42996.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A4D1E9 |
#43: Protein | Mass: 47086.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q9HC36, Transferases; Transferring one-carbon groups; Methyltransferases |
-RNA chain , 2 types, 2 molecules AB
#40: RNA chain | Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1025814679 |
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#44: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021 |
-Non-polymers , 3 types, 50 molecules
#52: Chemical | ChemComp-MG / #53: Chemical | ChemComp-ZN / | #54: Chemical | ChemComp-PNS / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human 39S mitoribosome assembly intermediates, state 1 Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||
3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18134 / Symmetry type: POINT |