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- EMDB-4938: C.elegans NAC-ribosomal 60S complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4938
TitleC.elegans NAC-ribosomal 60S complex
Map data
Sample
  • Complex: C.elegans NAC in complex with ribosomal 60S subunit
    • Protein or peptide: Nascent chain associated complex subunit alpha
    • Protein or peptide: Nascent chain associated complex subunit beta
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKobayashi K / Jomaa A / Ban N
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_163478 Switzerland
Swiss National Science Foundation51NF40_141735 Switzerland
CitationJournal: 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
DepositionMay 7, 2019-
Header (metadata) releaseAug 14, 2019-
Map releaseAug 14, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4938.png

Downloads & links

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Map

FileDownload / File: emd_4938.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.055
Minimum - Maximum-0.131196 - 0.34256294
Average (Standard dev.)0.0028869053 (±0.023641583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1310.3430.003

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Supplemental data

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Sample components

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Entire : C.elegans NAC in complex with ribosomal 60S subunit

EntireName: C.elegans NAC in complex with ribosomal 60S subunit
Components
  • Complex: C.elegans NAC in complex with ribosomal 60S subunit
    • Protein or peptide: Nascent chain associated complex subunit alpha
    • Protein or peptide: Nascent chain associated complex subunit beta

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Supramolecule #1: C.elegans NAC in complex with ribosomal 60S subunit

SupramoleculeName: C.elegans NAC in complex with ribosomal 60S subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Nascent chain associated complex subunit alpha

MacromoleculeName: Nascent chain associated complex subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Nascent chain associated complex subunit beta

MacromoleculeName: Nascent chain associated complex subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDSKAIAERI KKLQAQQEHV RIGGKGTPRR KKKVIHKTAA ADDKKLQSNL KKLSVTNIPG IEEVNMIKDD GTVIHFNNPK VQTSVPANTF SVTGSADNKQ ITEMLPGILN QLGPESLTHL KKLANNVTKL GPDGKGEDED VPELVGDFDA ASKNETKADE Q

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Sugar embeddingMaterial: ice
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43971
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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