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- EMDB-2646: Structure of the mammalian ribosome-Sec61 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2646
TitleStructure of the mammalian ribosome-Sec61 complex
Map dataMammalian ribosome in complex with Sec61. Class with eEF2
Sample
  • Sample: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing.
  • Complex: Mammalian ribosome
  • Protein or peptide: Sec61
Keywordstranslation / ribosome / mammalian / sec61
Function / homology
Function and homology information


: / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Protein hydroxylation / Degradation of CDH1 / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / multicellular organism development ...: / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Protein hydroxylation / Degradation of CDH1 / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / multicellular organism development / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation at presynapse / cellular response to actinomycin D / regulation of G1 to G0 transition / protein-DNA complex disassembly / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / alpha-beta T cell differentiation / G1 to G0 transition / cysteine-type endopeptidase activator activity involved in apoptotic process / regulation of establishment of cell polarity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / cytoplasmic side of rough endoplasmic reticulum membrane / organelle membrane / laminin receptor activity / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / BH3 domain binding / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of GTPase activity / regulation of cell division / protein serine/threonine kinase inhibitor activity / ubiquitin ligase inhibitor activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / phagocytic cup / positive regulation of intrinsic apoptotic signaling pathway / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rough endoplasmic reticulum / laminin binding / gastrulation / signaling adaptor activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cytosolic ribosome / rescue of stalled cytosolic ribosome / SH2 domain binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cyclin binding / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of smoothened signaling pathway / maturation of SSU-rRNA / small-subunit processome / cellular response to glucose stimulus / positive regulation of protein-containing complex assembly / negative regulation of cell growth / positive regulation of protein phosphorylation / receptor tyrosine kinase binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cellular response to growth factor stimulus / spindle / transcription coactivator binding / protein tag activity / cytoplasmic ribonucleoprotein granule / rRNA processing / rhythmic process / regulation of translation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / heparin binding / large ribosomal subunit / ribosomal small subunit assembly / ribosome biogenesis / presynapse / virus receptor activity / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / S27a-like superfamily / Ribosomal protein L44e signature. / 40S Ribosomal protein S10 / 60S ribosomal protein L18a/ L20, eukaryotes / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal protein S27a / Ribosomal L40e family / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / : / Ribosomal protein L30/YlxQ / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein L18e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / :
Similarity search - Domain/homology
Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS19 / Uncharacterized protein / 40S ribosomal protein S4 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS10 ...Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS19 / Uncharacterized protein / 40S ribosomal protein S4 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS7 / 40S ribosomal protein S8 / : / Uncharacterized protein / Ubiquitin-ribosomal protein eS31 fusion protein / 40S ribosomal protein S7 / Large ribosomal subunit protein eL18 / Ribosomal protein L26 / Ribosomal protein L15 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L13 / : / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL18
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVoorhees RM / Fernandez IS / Scheres SHW / Hegde R
CitationJournal: Cell / Year: 2014
Title: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
Authors: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde /
Abstract: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.
History
DepositionMay 13, 2014-
Header (metadata) releaseJun 18, 2014-
Map releaseJul 16, 2014-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j7p
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2646.png

Downloads & links

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Map

FileDownload / File: emd_2646.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian ribosome in complex with Sec61. Class with eEF2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 420 pix.
= 562.8 Å		1.34 Å/pix.
x 420 pix.
= 562.8 Å		1.34 Å/pix.
x 420 pix.
= 562.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.58023405 - 0.91271955
Average (Standard dev.)0.00144487 (±0.02510119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 562.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z562.800562.800562.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.5800.9130.001

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Supplemental data

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Supplemental map: emd 2646 half map 1.map

Fileemd_2646_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 2646 half map 2.map

Fileemd_2646_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mammalian ribosome in complex with Sec61 with the large subunit (...

EntireName: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing.
Components
  • Sample: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing.
  • Complex: Mammalian ribosome
  • Protein or peptide: Sec61

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Supramolecule #1000: Mammalian ribosome in complex with Sec61 with the large subunit (...

SupramoleculeName: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing.
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Mammalian ribosome

SupramoleculeName: Mammalian ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: Pig / Tissue: pancreas

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Macromolecule #1: Sec61

MacromoleculeName: Sec61 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: domestic pig

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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: 7.5
Details: 50mM hepes, 200mM K-acetate, 15mM Mg-acetate, 1mM DTT
GridDetails: Quantifoil R2/2 400 mesh copper grids.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV
Method: 3uL of sampled was incubated on the grid for 30 seconds before blotting for 9 second

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateApr 7, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1900 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 80019

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