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Yorodumi- EMDB-10978: The structure of the mitoribosome from Neurospora crassa with tRN... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10978 | |||||||||||||||
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Title | The structure of the mitoribosome from Neurospora crassa with tRNA bound to the E-site | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information 3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / nuclear pore inner ring / nuclear pore organization / mitochondrial genome maintenance / ATPase inhibitor activity / ribonuclease III activity / negative regulation of ATP-dependent activity / fungal-type vacuole / DNA strand exchange activity ...3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / nuclear pore inner ring / nuclear pore organization / mitochondrial genome maintenance / ATPase inhibitor activity / ribonuclease III activity / negative regulation of ATP-dependent activity / fungal-type vacuole / DNA strand exchange activity / mitochondrial large ribosomal subunit / structural constituent of nuclear pore / positive regulation of translational fidelity / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / RNA processing / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / double-stranded RNA binding / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / single-stranded DNA binding / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Neurospora crassa OR74A (fungus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Amunts A / Itoh Y / Naschberger A | |||||||||||||||
Funding support | Sweden, European Union, 4 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi. Authors: Yuzuru Itoh / Andreas Naschberger / Narges Mortezaei / Johannes M Herrmann / Alexey Amunts / Abstract: Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each ...Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation. | |||||||||||||||
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_10978.map.gz | 143.9 MB | EMDB map data format | |
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Header (meta data) | emd-10978-v30.xml emd-10978.xml | 108.9 KB 108.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10978_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10978.png | 75.4 KB | ||
Masks | emd_10978_msk_1.map | 244.1 MB | Mask map | |
Others | emd_10978_additional_1.map.gz emd_10978_half_map_1.map.gz emd_10978_half_map_2.map.gz | 142.9 MB 194.7 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10978 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10978 | HTTPS FTP |
-Validation report
Summary document | emd_10978_validation.pdf.gz | 557.1 KB | Display | EMDB validaton report |
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Full document | emd_10978_full_validation.pdf.gz | 556.2 KB | Display | |
Data in XML | emd_10978_validation.xml.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10978 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10978 | HTTPS FTP |
-Related structure data
Related structure data | 6ywxMC 6yw5C 6yweC 6ywsC 6ywvC 6ywyC 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_10978.map.gz / Format: CCP4 / Size: 244.1 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: 1.06 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_10978_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Consensus map of the mitoribosome from Neurospora crassa...
File | emd_10978_additional_1.map | ||||||||||||
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Annotation | Consensus map of the mitoribosome from Neurospora crassa with tRNA bound to the E-site | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10978_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10978_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitoribosome of Neurospora crassa with tRNA in the E-site
+Supramolecule #1: Mitoribosome of Neurospora crassa with tRNA in the E-site
+Macromolecule #1: 23S rRNA
+Macromolecule #78: 16S rRNA
+Macromolecule #79: tRNA E-site
+Macromolecule #2: 60S ribosomal protein L2
+Macromolecule #3: 60S ribosomal protein L3
+Macromolecule #4: 60S ribosomal protein L4, variant
+Macromolecule #5: 50S ribosomal protein L5
+Macromolecule #6: 60S ribosomal protein L6
+Macromolecule #7: RIBOSOMAL_L9 domain-containing protein
+Macromolecule #8: uL10m
+Macromolecule #9: 60S ribosomal protein L19
+Macromolecule #10: Ribosomal protein L13
+Macromolecule #11: 50S ribosomal protein L14
+Macromolecule #12: 50S ribosomal subunit protein L15
+Macromolecule #13: 60S ribosomal protein L16
+Macromolecule #14: 50S ribosomal protein L17
+Macromolecule #15: Mitochondrial ribosomal protein
+Macromolecule #16: Aconitate hydratase
+Macromolecule #17: Mitochondrial large ribosomal subunit
+Macromolecule #18: Mitochondrial ribosomal protein subunit L23
+Macromolecule #19: KOW domain-containing protein
+Macromolecule #20: bL27m
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: 54S ribosomal protein L4, mitochondrial
+Macromolecule #23: 50S ribosomal protein L30
+Macromolecule #24: bL31m
+Macromolecule #25: Mitochondrial ribosomal protein subunit L32
+Macromolecule #26: bL33m
+Macromolecule #27: Related to ribosomal protein L34, mitochondrial
+Macromolecule #28: Ribosomal protein
+Macromolecule #29: Mitochondrial large ribosomal subunit YmL35
+Macromolecule #30: mL40
+Macromolecule #31: mL41
+Macromolecule #32: Mitochondrial ribosomal protein L43
+Macromolecule #33: 60S ribosomal protein L3
+Macromolecule #34: 50S ribosomal subunit L30
+Macromolecule #35: mL49
+Macromolecule #36: mL50
+Macromolecule #37: Mitochondrial ribosomal protein L44
+Macromolecule #38: mL54
+Macromolecule #39: RNase III domain-containing protein
+Macromolecule #40: 60S ribosomal protein L20
+Macromolecule #41: Mitochondrial 60S ribosomal protein L25
+Macromolecule #42: 54S ribosomal protein L31, mitochondrial
+Macromolecule #43: mL67
+Macromolecule #44: bS1m
+Macromolecule #45: Mito ribosomal protein S2
+Macromolecule #46: Ribosomal protein S5, mitochondrial
+Macromolecule #47: Mito ribosomal protein S4
+Macromolecule #48: 37S ribosomal protein S5
+Macromolecule #49: Mito ribosomal protein S6
+Macromolecule #50: Ribosomal_S7 domain-containing protein
+Macromolecule #51: 40S ribosomal protein S8
+Macromolecule #52: 37S ribosomal protein S9, mitochondrial
+Macromolecule #53: 37S ribosomal protein S10, mitochondrial
+Macromolecule #54: Mitochondrial ribosomal protein subunit S18
+Macromolecule #55: Mitochondrial 30S ribosomal protein S12
+Macromolecule #56: 40S ribosomal protein S13
+Macromolecule #57: Mitochondrial 40S ribosomal protein MRP2
+Macromolecule #58: Ribosomal protein S15
+Macromolecule #59: Ribosomal protein S16, mitochondrial
+Macromolecule #60: Mitochondrial 37S ribosomal protein S17
+Macromolecule #61: Mito ribosomal protein S18
+Macromolecule #62: Mitochondrial ribosomal protein S19
+Macromolecule #63: Mito ribosomal protein S21
+Macromolecule #64: 37S ribosomal protein S25, mitochondrial
+Macromolecule #65: mS26
+Macromolecule #66: mS27
+Macromolecule #67: Mitochondrial ribosomal protein DAP3
+Macromolecule #68: mS33
+Macromolecule #69: 37S ribosomal protein S24, mitochondrial
+Macromolecule #70: 37S ribosomal protein mrp10, mitochondrial
+Macromolecule #71: DUF1713 domain-containing protein
+Macromolecule #72: IGR domain-containing protein
+Macromolecule #73: Fe superoxide dismutase
+Macromolecule #74: mS45
+Macromolecule #75: mS46
+Macromolecule #76: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
+Macromolecule #77: IF1
+Macromolecule #80: 60S ribosomal protein L1
+Macromolecule #81: L51_S25_CI-B8 domain-containing protein
+Macromolecule #82: MAGNESIUM ION
+Macromolecule #83: SPERMINE
+Macromolecule #84: POTASSIUM ION
+Macromolecule #85: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #86: ZINC ION
+Macromolecule #87: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.7 nm | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number real images: 3172 / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |