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- EMDB-2644: Structure of the mammalian ribosome-Sec61 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2644
TitleStructure of the mammalian ribosome-Sec61 complex
Map dataMammalian ribosome in complex with Sec61. Translating active class with mRNA and hybrid tRNAs
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


regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : / L13a-mediated translational silencing of Ceruloplasmin expression ...regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : / 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) / pronephric nephron development / protein insertion into ER membrane / malate dehydrogenase / protein-transporting ATPase activity / L-malate dehydrogenase (NAD+) activity / embryonic brain development / carboxylic acid metabolic process / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / ribosomal subunit / negative regulation of RNA splicing / neural crest cell differentiation / alpha-beta T cell differentiation / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / translation at presynapse / negative regulation of phagocytosis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / positive regulation of mitochondrial depolarization / organelle membrane / negative regulation of Wnt signaling pathway / negative regulation of translational frameshifting / BH3 domain binding / regulation of cell division / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of signal transduction by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / phagocytic cup / protein localization to nucleus / membrane => GO:0016020 / protein targeting / 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) / positive regulation of intrinsic apoptotic signaling pathway / rough endoplasmic reticulum / laminin binding / translation regulator activity / tricarboxylic acid cycle / signaling adaptor activity / gastrulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cytosolic ribosome / rescue of stalled ribosome / positive regulation of GTPase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / cyclin binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / mRNA 3'-UTR binding / negative regulation of smoothened signaling pathway / maturation of SSU-rRNA / neural tube closure / small-subunit processome / positive regulation of protein-containing complex assembly / cellular response to glucose stimulus / transcription coactivator binding / cellular response to gamma radiation / negative regulation of cell growth / cellular response to growth factor stimulus / maintenance of translational fidelity / receptor tyrosine kinase binding / calcium channel activity / modification-dependent protein catabolic process / spindle / mRNA 5'-UTR binding
Similarity search - Function
: / Malate dehydrogenase, type 3 / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex ...: / Malate dehydrogenase, type 3 / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30
Similarity search - Domain/homology
Ribosomal protein L15 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S27 / 40S ribosomal protein S6 / 40S ribosomal protein S10 / 40S ribosomal protein S15a ...Ribosomal protein L15 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S27 / 40S ribosomal protein S6 / 40S ribosomal protein S10 / 40S ribosomal protein S15a / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L13a isoform 1 / 60S ribosomal protein L36a / Ribosomal protein / 60S ribosomal protein L8 / 40S ribosomal protein S9 isoform a / 60S ribosomal protein L36 / 40S ribosomal protein S11 / Ribosomal protein L37 / 40S ribosomal protein S25 / Ribosomal protein L19 / 60S ribosomal protein L23 / 60S ribosomal protein L7 / 40S ribosomal protein S30 / Protein transport protein Sec61 subunit gamma / 60S ribosomal protein L37a / Malate dehydrogenase / 60S ribosomal protein L28 isoform 2 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL24 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L13 / SEC61 translocon alpha 1 subunit / Large ribosomal subunit protein eL30 / Ribosomal protein L26 / Large ribosomal subunit protein eL39 / 40S ribosomal protein S4 / Ribosomal protein L18 / Ubiquitin-ribosomal protein eS31 fusion protein / 60S ribosomal protein L7a / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS13 / 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 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL29
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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
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  • 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-3j7r
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2644.png

Downloads & links

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Map

FileDownload / File: emd_2644.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian ribosome in complex with Sec61. Translating active class with mRNA and hybrid tRNAs
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-0.39422372 - 0.67518675
Average (Standard dev.)0.00143454 (±0.02157907)
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-0.3940.6750.001

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Supplemental data

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Supplemental map: emdb 2644 half map 1.map

Fileemdb_2644_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emdb 2644 half map 2.map

Fileemdb_2644_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: domestic 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: 3.9 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 80019

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