[English] 日本語
![](img/lk-miru.gif)
- EMDB-12868: Structure of a human mitochondrial ribosome large subunit assembl... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-12868 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset2). | ||||||||||||||||||
![]() | Global refinement map. | ||||||||||||||||||
![]() |
| ||||||||||||||||||
![]() | Mitochondria / Ribosome / Biogenesis / GTPase / NSUN4 / MTERF4 | ||||||||||||||||||
Function / homology | ![]() rRNA modification in the mitochondrion / 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 modification in the mitochondrion / 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 / mRNA binding / nucleotide binding / synapse / calcium ion binding / regulation of DNA-templated transcription / nucleolus / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
![]() | Hillen HS / Lavdovskaia E | ||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||
![]() | ![]() Title: Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling. Authors: Hauke S Hillen / Elena Lavdovskaia / Franziska Nadler / Elisa Hanitsch / Andreas Linden / Katherine E Bohnsack / Henning Urlaub / Ricarda Richter-Dennerlein / ![]() Abstract: Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by ...Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint. | ||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 112.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 81.5 KB 81.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.4 KB | Display | ![]() |
Images | ![]() | 108 KB | ||
Masks | ![]() | 163.6 MB | ![]() | |
Filedesc metadata | ![]() | 16.8 KB | ||
Others | ![]() ![]() ![]() | 13.5 MB 113.4 MB 113.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7of3MC ![]() 7of0C ![]() 7of2C ![]() 7of4C ![]() 7of5C ![]() 7of6C ![]() 7of7C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Global refinement map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Post-processed map.
File | emd_12868_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post-processed map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Refinement half-map 1.
File | emd_12868_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Refinement half-map 1. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Refinement half-map 2.
File | emd_12868_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Refinement half-map 2. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : Human mitochondrial ribosome large subunit assembly intermediate ...
+Supramolecule #1: Human mitochondrial ribosome 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: 5-methylcytosine rRNA methyltransferase NSUN4
+Macromolecule #14: 39S ribosomal protein L2, mitochondrial
+Macromolecule #15: 39S ribosomal protein L3, mitochondrial
+Macromolecule #16: 39S ribosomal protein L4, mitochondrial
+Macromolecule #17: Transcription termination factor 4, mitochondrial
+Macromolecule #18: 39S ribosomal protein L9, mitochondrial
+Macromolecule #19: 39S ribosomal protein L10, mitochondrial
+Macromolecule #20: 39S ribosomal protein L11, mitochondrial
+Macromolecule #21: 39S ribosomal protein L13, mitochondrial
+Macromolecule #22: 39S ribosomal protein L14, mitochondrial
+Macromolecule #23: 39S ribosomal protein L15, mitochondrial
+Macromolecule #24: 39S ribosomal protein L16, mitochondrial
+Macromolecule #25: 39S ribosomal protein L17, mitochondrial
+Macromolecule #26: 39S ribosomal protein L18, mitochondrial
+Macromolecule #27: 39S ribosomal protein L19, mitochondrial
+Macromolecule #28: 39S ribosomal protein L20, mitochondrial
+Macromolecule #29: 39S ribosomal protein L21, mitochondrial
+Macromolecule #30: 39S ribosomal protein L22, mitochondrial
+Macromolecule #31: 39S ribosomal protein L23, mitochondrial
+Macromolecule #32: 39S ribosomal protein L24, mitochondrial
+Macromolecule #33: 39S ribosomal protein L27, mitochondrial
+Macromolecule #34: 39S ribosomal protein L28, mitochondrial
+Macromolecule #35: 39S ribosomal protein L47, mitochondrial
+Macromolecule #36: 39S ribosomal protein L30, mitochondrial
+Macromolecule #37: 39S ribosomal protein L42, mitochondrial
+Macromolecule #38: 39S ribosomal protein L43, mitochondrial
+Macromolecule #39: 39S ribosomal protein L44, mitochondrial
+Macromolecule #40: 39S ribosomal protein L45, mitochondrial
+Macromolecule #41: 39S ribosomal protein L46, mitochondrial
+Macromolecule #42: 39S ribosomal protein L48, mitochondrial
+Macromolecule #43: 39S ribosomal protein L49, mitochondrial
+Macromolecule #44: 39S ribosomal protein L50, mitochondrial
+Macromolecule #45: 39S ribosomal protein L51, mitochondrial
+Macromolecule #46: 39S ribosomal protein L52, mitochondrial
+Macromolecule #47: 39S ribosomal protein L53, mitochondrial
+Macromolecule #48: 39S ribosomal protein L55, mitochondrial
+Macromolecule #49: Ribosomal protein 63, mitochondrial
+Macromolecule #50: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #51: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #52: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #53: 39S ribosomal protein S30, mitochondrial
+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 #11: 16S ribosomal RNA
+Macromolecule #12: Mitochondrial tRNAVal
+Macromolecule #57: ZINC ION
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Model: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.25 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 37.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.3 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |