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Yorodumi- EMDB-13329: Structure of the human mitoribosomal large subunit in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13329 | |||||||||
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Title | Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP | |||||||||
Map data | Postprocessed map | |||||||||
Sample |
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Function / homology | Function and homology information regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / rRNA methyltransferase activity / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / mitochondrial ribosome assembly / 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 / protein targeting to mitochondrion / mitochondrial fission / camera-type eye development / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / rRNA methylation / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / acyl binding / anatomical structure morphogenesis / Complex I biogenesis / acyl carrier activity / Respiratory electron transport / RNA processing / mitochondrial respiratory chain complex I assembly / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / : / ribosomal large subunit biogenesis / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / cellular response to leukemia inhibitory factor / methyltransferase activity / Mitochondrial protein degradation / fatty acid binding / mitochondrial membrane / aerobic respiration / fibrillar center / fatty acid biosynthetic process / rRNA processing / cell junction / double-stranded RNA binding / double-stranded DNA binding / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / synapse / calcium ion binding / regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Chandrasekaran V / Desai N / Burton NO / Yang H / Price J / Miska EA / Ramakrishnan V | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Elife / Year: 2021 Title: Visualizing formation of the active site in the mitochondrial ribosome. Authors: Viswanathan Chandrasekaran / Nirupa Desai / Nicholas O Burton / Hanting Yang / Jon Price / Eric A Miska / V Ramakrishnan / Abstract: Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved ...Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13329.map.gz | 54.9 MB | EMDB map data format | |
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Header (meta data) | emd-13329-v30.xml emd-13329.xml | 79.2 KB 79.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13329_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_13329.png | 207.3 KB | ||
Masks | emd_13329_msk_1.map | 512 MB | Mask map | |
Others | emd_13329_additional_1.map.gz emd_13329_additional_2.map.gz emd_13329_half_map_1.map.gz emd_13329_half_map_2.map.gz | 407.9 MB 454.5 MB 412.5 MB 412.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13329 | HTTPS FTP |
-Validation report
Summary document | emd_13329_validation.pdf.gz | 477.3 KB | Display | EMDB validaton report |
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Full document | emd_13329_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | emd_13329_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_13329_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13329 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13329 | HTTPS FTP |
-Related structure data
Related structure data | 7pd3MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13329.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13329_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Refined map
File | emd_13329_additional_1.map | ||||||||||||
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Annotation | Refined map | ||||||||||||
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Density Histograms |
-Additional map: deepEMhancer map for interpretation
File | emd_13329_additional_2.map | ||||||||||||
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Annotation | deepEMhancer map for interpretation | ||||||||||||
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Density Histograms |
-Half map: Half2 map
File | emd_13329_half_map_1.map | ||||||||||||
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Annotation | Half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 map
File | emd_13329_half_map_2.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human mitoribosomal large subunit assembly intermediate
+Supramolecule #1: human mitoribosomal large subunit assembly intermediate
+Macromolecule #1: 39S ribosomal protein L32, mitochondrial
+Macromolecule #2: 39S ribosomal protein L33, mitochondrial
+Macromolecule #3: 39S ribosomal protein L34, mitochondrial
+Macromolecule #4: 39S ribosomal protein L35, mitochondrial
+Macromolecule #5: 39S ribosomal protein L36, mitochondrial
+Macromolecule #6: 39S ribosomal protein L37, mitochondrial
+Macromolecule #7: 39S ribosomal protein L38, mitochondrial
+Macromolecule #8: 39S ribosomal protein L39, mitochondrial
+Macromolecule #9: 39S ribosomal protein L40, mitochondrial
+Macromolecule #10: 39S ribosomal protein L41, mitochondrial
+Macromolecule #13: 39S ribosomal protein L9, mitochondrial
+Macromolecule #14: 39S ribosomal protein L2, mitochondrial
+Macromolecule #15: 39S ribosomal protein L3, mitochondrial
+Macromolecule #16: 39S ribosomal protein L4, mitochondrial
+Macromolecule #17: 39S ribosomal protein L10, mitochondrial
+Macromolecule #18: 39S ribosomal protein L11, mitochondrial
+Macromolecule #19: 39S ribosomal protein L13, mitochondrial
+Macromolecule #20: 39S ribosomal protein L14, mitochondrial
+Macromolecule #21: 39S ribosomal protein L15, mitochondrial
+Macromolecule #22: 39S ribosomal protein L16, mitochondrial
+Macromolecule #23: 39S ribosomal protein L17, mitochondrial
+Macromolecule #24: 39S ribosomal protein L18, mitochondrial
+Macromolecule #25: 39S ribosomal protein L19, mitochondrial
+Macromolecule #26: 39S ribosomal protein L20, mitochondrial
+Macromolecule #27: 39S ribosomal protein L21, mitochondrial
+Macromolecule #28: 39S ribosomal protein L22, mitochondrial
+Macromolecule #29: 39S ribosomal protein L23, mitochondrial
+Macromolecule #30: 39S ribosomal protein L24, mitochondrial
+Macromolecule #31: 39S ribosomal protein L27, mitochondrial
+Macromolecule #32: 39S ribosomal protein L28, mitochondrial
+Macromolecule #33: 39S ribosomal protein L47, mitochondrial
+Macromolecule #34: 39S ribosomal protein L30, mitochondrial
+Macromolecule #35: 39S ribosomal protein L42, mitochondrial
+Macromolecule #36: 39S ribosomal protein L43, mitochondrial
+Macromolecule #37: 39S ribosomal protein L44, mitochondrial
+Macromolecule #38: 39S ribosomal protein L45, mitochondrial
+Macromolecule #39: 39S ribosomal protein L46, mitochondrial
+Macromolecule #40: 39S ribosomal protein L48, mitochondrial
+Macromolecule #41: 39S ribosomal protein L49, mitochondrial
+Macromolecule #42: 39S ribosomal protein L50, mitochondrial
+Macromolecule #43: 39S ribosomal protein L51, mitochondrial
+Macromolecule #44: 39S ribosomal protein L52, mitochondrial
+Macromolecule #45: 39S ribosomal protein L53, mitochondrial
+Macromolecule #46: 39S ribosomal protein L54, mitochondrial
+Macromolecule #47: 39S ribosomal protein L55, mitochondrial
+Macromolecule #48: Ribosomal protein 63, mitochondrial
+Macromolecule #49: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #50: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #51: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #52: 39S ribosomal protein S30, mitochondrial
+Macromolecule #53: mL65
+Macromolecule #54: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #55: MIEF1 upstream open reading frame protein
+Macromolecule #56: Acyl carrier protein, mitochondrial
+Macromolecule #57: Transcription termination factor 4, mitochondrial
+Macromolecule #58: 5-methylcytosine rRNA methyltransferase NSUN4
+Macromolecule #59: Mitochondrial ribosome-associated GTPase 1
+Macromolecule #11: 16S rRNA
+Macromolecule #12: mt-tRNAVal
+Macromolecule #60: ZINC ION
+Macromolecule #61: ADENOSINE-5'-MONOPHOSPHATE
+Macromolecule #62: URIDINE-5'-MONOPHOSPHATE
+Macromolecule #63: CYTIDINE-5'-MONOPHOSPHATE
+Macromolecule #64: O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #65: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #66: PSEUDOURIDINE-5'-MONOPHOSPHATE
+Macromolecule #67: MAGNESIUM ION
+Macromolecule #68: 4'-PHOSPHOPANTETHEINE
+Macromolecule #69: S-ADENOSYLMETHIONINE
+Macromolecule #70: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 1.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |