[English] 日本語
![](img/lk-miru.gif)
- EMDB-17719: human mitoribosomal large subunit assembly intermediate 1 with GT... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 | |||||||||
![]() | full map, sharpened | |||||||||
![]() |
| |||||||||
![]() | mitochondria / maturation / biogenesis / ribosome / GTPBP7 / GTPBP10 / GTP Binding Protein 10 / OBGH2 / MTG1 / LSU | |||||||||
Function / homology | ![]() regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / rRNA methyltransferase activity / Respiratory electron transport / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / iron-sulfur cluster assembly complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / mitochondrial large ribosomal subunit binding / protein targeting to mitochondrion / Glyoxylate metabolism and glycine degradation / mitochondrial fission / camera-type eye development / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial large ribosomal subunit / 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 / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / anatomical structure morphogenesis / 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 / methyltransferase activity / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / ribosome biogenesis / cell junction / chromosome / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / double-stranded DNA binding / endonuclease activity / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / synapse / calcium ion binding / regulation of DNA-templated transcription / nucleolus / GTP binding / magnesium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
![]() | Kummer E / Nguyen TG / Ritter C | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome. Authors: Thu Giang Nguyen / Christina Ritter / Eva Kummer / ![]() Abstract: Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ...Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 398.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 79.6 KB 79.6 KB | Display Display | ![]() |
Images | ![]() | 96.9 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Filedesc metadata | ![]() | 17 KB | ||
Others | ![]() ![]() ![]() | 212.1 MB 391.2 MB 391.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pk0MC ![]() 8qsjC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | full map, sharpened | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: full map, unsharpened
File | emd_17719_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | full map, unsharpened | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_17719_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_17719_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : large mitoribosomal subunit biogenesis intermediate with GTPBP10,...
+Supramolecule #1: large mitoribosomal subunit biogenesis intermediate with GTPBP10,...
+Macromolecule #1: 39S ribosomal protein L32, mitochondrial
+Macromolecule #2: 39S ribosomal protein L22, mitochondrial
+Macromolecule #3: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #4: 39S ribosomal protein L33, mitochondrial
+Macromolecule #5: 39S ribosomal protein L23, mitochondrial
+Macromolecule #6: MIEF1 upstream open reading frame protein
+Macromolecule #7: 39S ribosomal protein L34, mitochondrial
+Macromolecule #8: 39S ribosomal protein L24, mitochondrial
+Macromolecule #9: Acyl carrier protein, mitochondrial
+Macromolecule #10: 39S ribosomal protein L35, mitochondrial
+Macromolecule #11: 39S ribosomal protein L27, mitochondrial
+Macromolecule #12: 5-methylcytosine rRNA methyltransferase NSUN4
+Macromolecule #13: 39S ribosomal protein L37, mitochondrial
+Macromolecule #14: 39S ribosomal protein L28, mitochondrial
+Macromolecule #15: Transcription termination factor 4, mitochondrial
+Macromolecule #16: 39S ribosomal protein L38, mitochondrial
+Macromolecule #17: 39S ribosomal protein L47, mitochondrial
+Macromolecule #18: Mitochondrial ribosome-associated GTPase 1
+Macromolecule #19: 39S ribosomal protein L39, mitochondrial
+Macromolecule #20: 39S ribosomal protein L30, mitochondrial
+Macromolecule #21: 39S ribosomal protein L40, mitochondrial
+Macromolecule #22: 39S ribosomal protein L42, mitochondrial
+Macromolecule #23: 39S ribosomal protein L41, mitochondrial
+Macromolecule #24: Large ribosomal subunit protein mL43
+Macromolecule #26: 39S ribosomal protein L44, mitochondrial
+Macromolecule #28: 39S ribosomal protein L45, mitochondrial
+Macromolecule #29: 39S ribosomal protein L2, mitochondrial
+Macromolecule #30: 39S ribosomal protein L46, mitochondrial
+Macromolecule #31: 39S ribosomal protein L3, mitochondrial
+Macromolecule #32: 39S ribosomal protein L48, mitochondrial
+Macromolecule #33: 39S ribosomal protein L4, mitochondrial
+Macromolecule #34: 39S ribosomal protein L49, mitochondrial
+Macromolecule #35: 39S ribosomal protein L9, mitochondrial
+Macromolecule #36: 39S ribosomal protein L50, mitochondrial
+Macromolecule #37: 39S ribosomal protein L10, mitochondrial
+Macromolecule #38: 39S ribosomal protein L51, mitochondrial
+Macromolecule #39: 39S ribosomal protein L11, mitochondrial
+Macromolecule #40: 39S ribosomal protein L52, mitochondrial
+Macromolecule #41: 39S ribosomal protein L13, mitochondrial
+Macromolecule #42: 39S ribosomal protein L53, mitochondrial
+Macromolecule #43: 39S ribosomal protein L14, mitochondrial
+Macromolecule #44: 39S ribosomal protein L54, mitochondrial
+Macromolecule #45: 39S ribosomal protein L15, mitochondrial
+Macromolecule #46: 39S ribosomal protein L55, mitochondrial
+Macromolecule #47: 39S ribosomal protein L16, mitochondrial
+Macromolecule #48: Ribosomal protein 63, mitochondrial
+Macromolecule #49: 39S ribosomal protein L17, mitochondrial
+Macromolecule #50: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #51: 39S ribosomal protein L18, mitochondrial
+Macromolecule #52: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #53: 39S ribosomal protein L19, mitochondrial
+Macromolecule #54: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #55: 39S ribosomal protein L20, mitochondrial
+Macromolecule #56: 39S ribosomal protein S30, mitochondrial
+Macromolecule #57: 39S ribosomal protein L21, mitochondrial
+Macromolecule #58: GTP-binding protein 10
+Macromolecule #25: 16S rRNA + pre-H68-71 segment
+Macromolecule #27: CP tRNA-Val
+Macromolecule #59: ZINC ION
+Macromolecule #60: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYL...
+Macromolecule #61: S-ADENOSYLMETHIONINE
+Macromolecule #62: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #63: MAGNESIUM ION
+Macromolecule #64: POTASSIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.6 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31656 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |