+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4938 | |||||||||
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Title | C.elegans NAC-ribosomal 60S complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Kobayashi K / Jomaa A / Ban N | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Mol Cell / Year: 2019 Title: Early Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC. Authors: Martin Gamerdinger / Kan Kobayashi / Annalena Wallisch / Stefan G Kreft / Carolin Sailer / Renate Schlömer / Nadine Sachs / Ahmad Jomaa / Florian Stengel / Nenad Ban / Elke Deuerling / Abstract: Cotranslational processing of newly synthesized proteins is fundamental for correct protein maturation. Protein biogenesis factors are thought to bind nascent polypeptides not before they exit the ...Cotranslational processing of newly synthesized proteins is fundamental for correct protein maturation. Protein biogenesis factors are thought to bind nascent polypeptides not before they exit the ribosomal tunnel. Here, we identify a nascent chain recognition mechanism deep inside the ribosomal tunnel by an essential eukaryotic cytosolic chaperone. The nascent polypeptide-associated complex (NAC) inserts the N-terminal tail of its β subunit (N-βNAC) into the ribosomal tunnel to sense substrates directly upon synthesis close to the peptidyl-transferase center. N-βNAC escorts the growing polypeptide to the cytosol and relocates to an alternate binding site on the ribosomal surface. Using C. elegans as an in vivo model, we demonstrate that the tunnel-probing activity of NAC is essential for organismal viability and critical to regulate endoplasmic reticulum (ER) protein transport by controlling ribosome-Sec61 translocon interactions. Thus, eukaryotic protein maturation relies on the early sampling of nascent chains inside the ribosomal tunnel. | |||||||||
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_4938.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-4938-v30.xml emd-4938.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_4938.png | 168.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4938 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4938 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4938.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : C.elegans NAC in complex with ribosomal 60S subunit
Entire | Name: C.elegans NAC in complex with ribosomal 60S subunit |
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Components |
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-Supramolecule #1: C.elegans NAC in complex with ribosomal 60S subunit
Supramolecule | Name: C.elegans NAC in complex with ribosomal 60S subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
-Macromolecule #1: Nascent chain associated complex subunit alpha
Macromolecule | Name: Nascent chain associated complex subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTGSTETRQK EVKEPQVDVS DDSDNEAVEQ ELTEEQRRVA EAAGLGDHID KQAKQSRSEK KARKLFSKLG LKQVTGVSRV CIRKSKNILF VINKPDVFKS PGSDTYIIFG EAKIEDLTQH AQMSAIENLK PTREAPQLKT VEEDENEDVE EDSTGIEEKD IELVISQANT ...String: MTGSTETRQK EVKEPQVDVS DDSDNEAVEQ ELTEEQRRVA EAAGLGDHID KQAKQSRSEK KARKLFSKLG LKQVTGVSRV CIRKSKNILF VINKPDVFKS PGSDTYIIFG EAKIEDLTQH AQMSAIENLK PTREAPQLKT VEEDENEDVE EDSTGIEEKD IELVISQANT TRNKAIRALK EADNDIVNAI MSLTM |
-Macromolecule #2: Nascent chain associated complex subunit beta
Macromolecule | Name: Nascent chain associated complex subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDSKAIAERI KKLQAQQEHV RIGGKGTPRR KKKVIHKTAA ADDKKLQSNL KKLSVTNIPG IEEVNMIKDD GTVIHFNNPK VQTSVPANTF SVTGSADNKQ ITEMLPGILN QLGPESLTHL KKLANNVTKL GPDGKGEDED VPELVGDFDA ASKNETKADE Q |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Sugar embedding | Material: ice |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43971 |