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- PDB-7oi6: Cryo-EM structure of late human 39S mitoribosome assembly interme... -
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Basic information
Entry | Database: PDB / ID: 7oi6 | |||||||||
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Title | Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1 | |||||||||
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![]() | RIBOSOME / 39S mitoribosome / ribosome biogenesis | |||||||||
Function / homology | ![]() 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 / Mitochondrial Fatty Acid Beta-Oxidation ...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 / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / translation release factor activity / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit / iron-sulfur cluster assembly complex / mitochondrial fission / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / mitochondrial translation / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / ribosomal large subunit binding / mitochondrial nucleoid / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / RNA processing / rescue of stalled ribosome / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / fatty acid binding / mitochondrial membrane / fibrillar center / rRNA processing / fatty acid biosynthetic process / ribosome biogenesis / double-stranded RNA binding / chromosome / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / endonuclease activity / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / cohesin loader activity / ATP-dependent H3-H4 histone complex chaperone activity / mitochondrial inner membrane / DNA clamp loader activity / RNA helicase activity / nuclear body / negative regulation of translation / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / mitochondrial matrix / protein domain specific binding / translation / ribonucleoprotein complex / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / calcium ion binding / GTP binding / nucleolus / magnesium ion binding / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
![]() | Cheng, J. / Berninghausen, O. / Beckmann, R. | |||||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 194.7 KB | Display | |
Data in CIF | ![]() | 345 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() |
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#33: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#34: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#39: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 59666.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 42996.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 47086.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() 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) ![]() |
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#44: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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 |
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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: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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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 |