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Yorodumi- EMDB-16407: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16407 | ||||||||||||||||||
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Title | Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on SSU head) | ||||||||||||||||||
Map data | local resolution filtered map mask refined on SSU head, fitted | ||||||||||||||||||
Sample |
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Keywords | mitochondrial translation / mRNA delivery / RIBOSOME | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||||||||
Authors | Singh V / Itoh Y / Amunts A | ||||||||||||||||||
Funding support | Sweden, European Union, 5 items
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Citation | Journal: To Be Published Title: Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome Authors: Singh V / Conor J / Itoh Y / Soto T / Fontanesi F / Couvillian M / Huynen M / Churchman S / Barrientos A / Amunts A | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16407.map.gz | 558.2 MB | EMDB map data format | |
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Header (meta data) | emd-16407-v30.xml emd-16407.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_16407.png | 86.7 KB | ||
Filedesc metadata | emd-16407.cif.gz | 4.1 KB | ||
Others | emd_16407_additional_1.map.gz emd_16407_additional_2.map.gz emd_16407_half_map_1.map.gz emd_16407_half_map_2.map.gz | 909.9 MB 817.1 MB 818.2 MB 817.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16407 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16407 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16407.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local resolution filtered map mask refined on SSU head, fitted | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpend map mask refined on SSU head, fitted
File | emd_16407_additional_1.map | ||||||||||||
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Annotation | unsharpend map mask refined on SSU head, fitted | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpend map mask refined on SSU head
File | emd_16407_additional_2.map | ||||||||||||
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Annotation | unsharpend map mask refined on SSU head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map mask refined on SSU head
File | emd_16407_half_map_1.map | ||||||||||||
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Annotation | half map mask refined on SSU head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map mask refined on SSU head
File | emd_16407_half_map_2.map | ||||||||||||
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Annotation | half map mask refined on SSU head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...
Entire | Name: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site |
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Components |
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-Supramolecule #1: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...
Supramolecule | Name: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41815 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |