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- EMDB-12920: Cryo-EM structure of late human 39S mitoribosome assembly interme... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12920 | |||||||||
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Title | Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 2 | |||||||||
![]() | local resolution filtered map | |||||||||
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![]() | 39S mitoribosome / ribosome biogenesis / RIBOSOME | |||||||||
Function / homology | ![]() negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / negative regulation of ribosome biogenesis / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / Respiratory electron transport / rRNA import into mitochondrion ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / negative regulation of ribosome biogenesis / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / Respiratory electron transport / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / 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 respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / anatomical structure morphogenesis / respiratory chain complex I / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / aerobic respiration / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / nucleolus / structural molecule activity / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Cheng J / Berninghausen O | |||||||||
![]() | ![]() Title: A distinct assembly pathway of the human 39S late pre-mitoribosome. Authors: Cheng J / Berninghausen O / Beckmann R | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
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Downloads & links
-EMDB archive
Map data | ![]() | 104.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 69.3 KB 69.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 154.2 KB | ||
Filedesc metadata | ![]() | 14.9 KB | ||
Others | ![]() | 140.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 479.3 KB | Display | ![]() |
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Full document | ![]() | 478.8 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oi7MC ![]() 7oi6C ![]() 7oi8C ![]() 7oi9C ![]() 7oiaC ![]() 7oibC ![]() 7oicC ![]() 7oidC ![]() 7oieC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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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Annotation | local resolution filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Human 39S mitoribosome assembly intermediates, state 2
+Supramolecule #1: Human 39S mitoribosome assembly intermediates, state 2
+Macromolecule #1: 39S ribosomal protein L2, mitochondrial
+Macromolecule #2: 39S ribosomal protein L3, mitochondrial
+Macromolecule #3: 39S ribosomal protein L4, mitochondrial
+Macromolecule #4: 39S ribosomal protein L9, mitochondrial
+Macromolecule #5: 39S ribosomal protein L10, mitochondrial
+Macromolecule #6: 39S ribosomal protein L11, mitochondrial
+Macromolecule #7: 39S ribosomal protein L13, mitochondrial
+Macromolecule #8: 39S ribosomal protein L14, mitochondrial
+Macromolecule #9: 39S ribosomal protein L15, mitochondrial
+Macromolecule #10: 39S ribosomal protein L16, mitochondrial
+Macromolecule #11: 39S ribosomal protein L17, mitochondrial
+Macromolecule #12: 39S ribosomal protein L18, mitochondrial
+Macromolecule #13: 39S ribosomal protein L19, mitochondrial
+Macromolecule #14: 39S ribosomal protein L20, mitochondrial
+Macromolecule #15: 39S ribosomal protein L21, mitochondrial
+Macromolecule #16: 39S ribosomal protein L22, mitochondrial
+Macromolecule #17: 39S ribosomal protein L23, mitochondrial
+Macromolecule #18: 39S ribosomal protein L24, mitochondrial
+Macromolecule #19: 39S ribosomal protein L27, mitochondrial
+Macromolecule #20: 39S ribosomal protein L28, mitochondrial
+Macromolecule #21: 39S ribosomal protein L47, mitochondrial
+Macromolecule #22: 39S ribosomal protein L30, mitochondrial
+Macromolecule #23: 39S ribosomal protein L32, mitochondrial
+Macromolecule #24: 39S ribosomal protein L33, mitochondrial
+Macromolecule #25: 39S ribosomal protein L34, mitochondrial
+Macromolecule #26: 39S ribosomal protein L35, mitochondrial
+Macromolecule #27: 39S ribosomal protein L37, mitochondrial
+Macromolecule #28: 39S ribosomal protein L38, mitochondrial
+Macromolecule #29: 39S ribosomal protein L39, mitochondrial
+Macromolecule #30: 39S ribosomal protein L40, mitochondrial
+Macromolecule #31: 39S ribosomal protein L41, mitochondrial
+Macromolecule #32: 39S ribosomal protein L42, mitochondrial
+Macromolecule #33: 39S ribosomal protein L43, mitochondrial
+Macromolecule #34: 39S ribosomal protein L44, mitochondrial
+Macromolecule #35: 39S ribosomal protein L45, mitochondrial
+Macromolecule #36: 39S ribosomal protein L46, mitochondrial
+Macromolecule #37: 39S ribosomal protein L48, mitochondrial
+Macromolecule #38: 39S ribosomal protein L49, mitochondrial
+Macromolecule #39: 39S ribosomal protein L50, mitochondrial
+Macromolecule #40: 39S ribosomal protein L51, mitochondrial
+Macromolecule #41: 39S ribosomal protein L52, mitochondrial
+Macromolecule #42: 39S ribosomal protein L53, mitochondrial
+Macromolecule #43: 39S ribosomal protein L54, mitochondrial
+Macromolecule #44: 39S ribosomal protein L55, mitochondrial
+Macromolecule #45: Ribosomal protein 63, mitochondrial
+Macromolecule #46: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #47: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #48: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #49: 39S ribosomal protein S30, mitochondrial
+Macromolecule #50: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #51: MIEF1 upstream open reading frame protein
+Macromolecule #52: Acyl carrier protein, mitochondrial
+Macromolecule #53: 16S rRNA
+Macromolecule #54: mitochondrial Val tRNA
+Macromolecule #55: ZINC ION
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: 4'-PHOSPHOPANTETHEINE
-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: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |