[English] 日本語
Yorodumi- EMDB-10985: The structure of the mitoribosome from Neurospora crassa with bou... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10985 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site | |||||||||||||||
Map data | Composite map for the P-tRNA bound state. | |||||||||||||||
Sample |
| |||||||||||||||
Function / homology | Function and homology information 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / DNA strand exchange activity / mitochondrial genome maintenance / negative regulation of ATP-dependent activity / ATPase inhibitor activity / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial ribosome ...3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / DNA strand exchange activity / mitochondrial genome maintenance / negative regulation of ATP-dependent activity / ATPase inhibitor activity / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / superoxide dismutase activity / RNA processing / rRNA processing / double-stranded RNA binding / large ribosomal subunit / single-stranded DNA binding / small ribosomal subunit / transferase activity / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mitochondrion / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Neurospora crassa (fungus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||||||||
Authors | Amunts A / Itoh Y / Naschberger A | |||||||||||||||
Funding support | Sweden, European Union, 4 items
| |||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10985.map.gz | 144.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10985-v30.xml emd-10985.xml | 109.8 KB 109.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10985_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10985.png | 81.2 KB | ||
Masks | emd_10985_msk_1.map | 244.1 MB | Mask map | |
Others | emd_10985_additional_1.map.gz emd_10985_half_map_1.map.gz emd_10985_half_map_2.map.gz | 143.1 MB 194.3 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10985 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10985 | HTTPS FTP |
-Validation report
Summary document | emd_10985_validation.pdf.gz | 514.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_10985_full_validation.pdf.gz | 513.8 KB | Display | |
Data in XML | emd_10985_validation.xml.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10985 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10985 | HTTPS FTP |
-Related structure data
Related structure data | 6ywyMC 6yw5C 6yweC 6ywsC 6ywvC 6ywxC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_10985.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Composite map for the P-tRNA bound state. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_10985_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Consensus map for the P-tRNA bound state.
File | emd_10985_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Consensus map for the P-tRNA bound state. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_10985_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_10985_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Mitoribosome of Neurospora crassa in the tRNA bound state (P-site).
+Supramolecule #1: Mitoribosome of Neurospora crassa in the tRNA bound state (P-site).
+Macromolecule #1: 23S rRNA
+Macromolecule #78: 16S rRNA
+Macromolecule #79: P-site-tRNA
+Macromolecule #80: mRNA
+Macromolecule #2: 60S ribosomal protein L2, mitochondrial
+Macromolecule #3: Related to ribosomal protein L3, mitochondrial
+Macromolecule #4: 60S ribosomal protein L4, variant
+Macromolecule #5: Related to ribosomal protein L5, mitochondrial
+Macromolecule #6: uL6m
+Macromolecule #7: RIBOSOMAL_L9 domain-containing protein
+Macromolecule #8: Related to ribosomal protein YmL11, mitochondrial
+Macromolecule #9: uL11m
+Macromolecule #10: uL13m
+Macromolecule #11: Ribosomal protein L14
+Macromolecule #12: Ribosomal protein L15
+Macromolecule #13: Related to ribosomal protein L16, mitochondrial
+Macromolecule #14: uL17m
+Macromolecule #15: bL19m
+Macromolecule #16: Related to ribosomal protein YmL49, mitochondrial
+Macromolecule #17: Mitochondrial large ribosomal subunit
+Macromolecule #18: uL23m
+Macromolecule #19: KOW domain-containing protein
+Macromolecule #20: Related to 60s ribosomal protein L2 (Mitochondrial)
+Macromolecule #21: bL28m
+Macromolecule #22: 54S ribosomal protein L4, mitochondrial
+Macromolecule #23: Related to ribosomal protein L30
+Macromolecule #24: Related to ribosomal protein YmL36, mitochondrial
+Macromolecule #25: Related to ribosomal protein YmL32 (Mitochondrial)
+Macromolecule #26: bL33m
+Macromolecule #27: Related to ribosomal protein L34, mitochondrial
+Macromolecule #28: Ribosomal protein
+Macromolecule #29: PEBP-like protein
+Macromolecule #30: mL40
+Macromolecule #31: mL41
+Macromolecule #32: L51_S25_CI-B8 domain-containing protein
+Macromolecule #33: Ribonuclease III
+Macromolecule #34: mL46
+Macromolecule #35: mL49
+Macromolecule #36: mL50
+Macromolecule #37: Probable ribosomal protein YmL44, mitochondrial
+Macromolecule #38: mL54
+Macromolecule #39: RNase III domain-containing protein
+Macromolecule #40: Related to ribosomal protein YmL20, mitochondrial
+Macromolecule #41: Mitoc_mL59 domain-containing protein
+Macromolecule #42: 54S ribosomal protein L31, mitochondrial
+Macromolecule #43: mL67
+Macromolecule #44: bS1m
+Macromolecule #45: Mito ribosomal protein S2
+Macromolecule #46: Ribosomal protein S5
+Macromolecule #47: S4 RNA-binding domain-containing protein
+Macromolecule #48: Related to ribosomal protein S5 (Mitochondrial)
+Macromolecule #49: Ribosomal protein S6
+Macromolecule #50: Ribosomal_S7 domain-containing protein
+Macromolecule #51: uS8m
+Macromolecule #52: uS9m
+Macromolecule #53: 30S ribosomal protein S10, mitochondrial
+Macromolecule #54: Translational machinery component
+Macromolecule #55: Ribosomal protein S12
+Macromolecule #56: Probable ribosomal protein S13
+Macromolecule #57: Mitochondrial 37S ribosomal protein MRP2
+Macromolecule #58: Related to ribosomal protein S15 (Mitochondrial)
+Macromolecule #59: bS16m
+Macromolecule #60: uS17m
+Macromolecule #61: Ribosomal protein S18
+Macromolecule #62: Ribosomal protein S19/S15
+Macromolecule #63: bS21m
+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: Protein FYV4, mitochondrial
+Macromolecule #73: Manganese and iron superoxide dismutase
+Macromolecule #74: mS45
+Macromolecule #75: mS46
+Macromolecule #76: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
+Macromolecule #77: IF1
+Macromolecule #81: Poly-Peptide
+Macromolecule #82: 60S ribosomal protein L1, mitochondrial
+Macromolecule #83: L51_S25_CI-B8 domain-containing protein
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: SPERMINE
+Macromolecule #86: POTASSIUM ION
+Macromolecule #87: ZINC ION
+Macromolecule #88: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #89: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
---|---|
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 |