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Yorodumi- EMDB-11845: Trypanosoma brucei mitochondrial ribosome large subunit assembly ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11845 | |||||||||||||||||||||
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Title | Trypanosoma brucei mitochondrial ribosome large subunit assembly intermediate | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information pseudouridine synthesis / pseudouridine synthase activity / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / post-transcriptional regulation of gene expression / cyclosporin A binding / mitochondrial translation / : ...pseudouridine synthesis / pseudouridine synthase activity / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / post-transcriptional regulation of gene expression / cyclosporin A binding / mitochondrial translation / : / acyl binding / acyl carrier activity / RNA processing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / lipid metabolic process / fatty acid biosynthetic process / large ribosomal subunit / protein folding / RNA helicase activity / rRNA binding / hydrolase activity / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Tobiasson V / Gahura O / Aibara S / Baradaran R / Zikova A / Amunts A | |||||||||||||||||||||
Funding support | Sweden, Czech Republic, 6 items
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Citation | Journal: EMBO J / Year: 2021 Title: Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit. Authors: Victor Tobiasson / Ondřej Gahura / Shintaro Aibara / Rozbeh Baradaran / Alena Zíková / Alexey Amunts / Abstract: Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased ...Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit. | |||||||||||||||||||||
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_11845.map.gz | 727.8 MB | EMDB map data format | |
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Header (meta data) | emd-11845-v30.xml emd-11845.xml | 96.3 KB 96.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11845_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_11845.png | 174.5 KB | ||
Others | emd_11845_half_map_1.map.gz emd_11845_half_map_2.map.gz | 673 MB 672.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11845 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11845 | HTTPS FTP |
-Validation report
Summary document | emd_11845_validation.pdf.gz | 375.5 KB | Display | EMDB validaton report |
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Full document | emd_11845_full_validation.pdf.gz | 374.7 KB | Display | |
Data in XML | emd_11845_validation.xml.gz | 27 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11845 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11845 | HTTPS FTP |
-Related structure data
Related structure data | 7aoiMC 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_11845.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_11845_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11845_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Trypanosoma brucei mitochondrial ribosome large subunit assembly ...
+Supramolecule #1: Trypanosoma brucei mitochondrial ribosome large subunit assembly ...
+Macromolecule #1: bL28m
+Macromolecule #2: uL29m
+Macromolecule #3: uL30m
+Macromolecule #4: bL32m
+Macromolecule #5: bL33m
+Macromolecule #7: Ribosomal protein L3 mitochondrial, putative
+Macromolecule #8: Ribosomal protein L4/L1 family
+Macromolecule #9: RIBOSOMAL_L9 domain-containing protein
+Macromolecule #10: Ribosomal protein L11,uL11m
+Macromolecule #11: 50S ribosomal protein L13
+Macromolecule #12: Ribosomal_L18e/L15P domain-containing protein
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: bL19m
+Macromolecule #15: bL20m
+Macromolecule #16: Ribosomal protein L21
+Macromolecule #17: Ribosomal protein L22p/L17e
+Macromolecule #18: Ribosomal protein L23
+Macromolecule #19: uL24m
+Macromolecule #20: mL41
+Macromolecule #21: mL42
+Macromolecule #22: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containi...
+Macromolecule #23: mL49
+Macromolecule #24: mL52
+Macromolecule #25: mL53
+Macromolecule #26: mL63
+Macromolecule #27: mL64,mL64
+Macromolecule #28: mL67
+Macromolecule #29: mL68,mL68,mL68
+Macromolecule #30: mL70
+Macromolecule #31: mL71
+Macromolecule #32: Tetratricopeptide repeat
+Macromolecule #33: mL74
+Macromolecule #34: Mitochondrial RNA binding complex 1 subunit
+Macromolecule #35: mL76
+Macromolecule #36: Chaperone protein DNAj, putative,mL77,Chaperone protein DNAj, putative
+Macromolecule #37: mL78
+Macromolecule #38: mL80
+Macromolecule #39: mL81
+Macromolecule #40: Peptidyl-prolyl cis-trans isomerase
+Macromolecule #41: mL84
+Macromolecule #42: mL85
+Macromolecule #43: mL86
+Macromolecule #44: mL87
+Macromolecule #45: mL89
+Macromolecule #46: LIM domain containing protein,mL90
+Macromolecule #47: Peptidyl-prolyl cis-trans isomerase
+Macromolecule #48: mL93
+Macromolecule #49: mL94
+Macromolecule #50: mL95
+Macromolecule #51: mL98
+Macromolecule #52: mL99
+Macromolecule #53: mL100,mL100
+Macromolecule #54: UNK1
+Macromolecule #55: UNK2
+Macromolecule #56: UNK3
+Macromolecule #57: UNK4
+Macromolecule #58: UNK5
+Macromolecule #59: UNK6/mt-LAF15_2
+Macromolecule #60: UNK7
+Macromolecule #61: UNK8
+Macromolecule #62: UNK9
+Macromolecule #63: UNK10
+Macromolecule #64: UNK11
+Macromolecule #65: mt-LAF7,mt-LAF7
+Macromolecule #66: DEAD-box helicase, putative,mt-LAF2
+Macromolecule #67: mt-LAF4
+Macromolecule #68: Acyl carrier protein
+Macromolecule #69: mt-LAF15_1
+Macromolecule #70: 50S ribosomal protein L14
+Macromolecule #71: mt-LAF8
+Macromolecule #72: mt-LAF14
+Macromolecule #73: RNA uridylyltransferase
+Macromolecule #74: GTP-binding protein, putative,mt-EngA
+Macromolecule #75: Complex1-LYR-like
+Macromolecule #76: mt-LAF12
+Macromolecule #77: SpoU rRNA Methylase family
+Macromolecule #78: Pseudouridylate synthase, putative
+Macromolecule #79: GTP-binding protein
+Macromolecule #80: Lipase (Class 3)
+Macromolecule #81: mL101
+Macromolecule #82: mt-LAF19
+Macromolecule #6: mt-LSU rRNA
+Macromolecule #83: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #84: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #85: ZINC ION
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #88: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.45 |
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 300.0 nm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 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 |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-7aoi: |