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- EMDB-5592: Electron cryo-microscopy of human 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-5592
TitleElectron cryo-microscopy of human 80S ribosome
Map dataReconstruction of H. sapiens 80S ribosome
Sample
  • Sample: Human 80S ribosome from PBMCs
  • Complex: 80S ribosome
Keywordseukarya eukaryotic ribosomal ribosome 80S protein RNA cryo-electron microscopy protein synthesis mass spectrometry human
Function / homology
Function and homology information


Synthesis of diphthamide-EEF2 / cytoplasmic translational elongation / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of formation of translation preinitiation complex ...Synthesis of diphthamide-EEF2 / cytoplasmic translational elongation / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / ribosomal protein import into nucleus / positive regulation of respiratory burst involved in inflammatory response / 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 intrinsic apoptotic signaling pathway in response to DNA damage / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / : / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / negative regulation of DNA repair / TORC2 complex binding / negative regulation of RNA splicing / mammalian oogenesis stage / GAIT complex / A band / supercoiled DNA binding / G1 to G0 transition / activation-induced cell death of T cells / oxidized purine DNA binding / NF-kappaB complex / middle ear morphogenesis / neural crest cell differentiation / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / alpha-beta T cell differentiation / ubiquitin-like protein conjugating enzyme binding / translation at presynapse / regulation of establishment of cell polarity / rRNA modification in the nucleus and cytosol / exit from mitosis / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / aggresome / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of peptidyl-serine phosphorylation / protein kinase A binding / optic nerve development / negative regulation of ubiquitin protein ligase activity / pigmentation / retinal ganglion cell axon guidance / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / homeostatic process / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / lung morphogenesis / Uptake and function of diphtheria toxin / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / male meiosis I / monocyte chemotaxis / Protein hydroxylation / BH3 domain binding / TOR signaling / cysteine-type endopeptidase activator activity involved in apoptotic process / SARS-CoV-1 modulates host translation machinery / regulation of cell division / iron-sulfur cluster binding / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / Selenocysteine synthesis / 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) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / blastocyst development
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 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 / Ubiquitin-like protein FUBI / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / S27a-like superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S10, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L19/L19e conserved site / : / : / Ribosomal protein L19e signature. / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e
Similarity search - Domain/homology
Large ribosomal subunit protein P1 / Large ribosomal subunit protein P2 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Elongation factor 2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 ...Large ribosomal subunit protein P1 / Large ribosomal subunit protein P2 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Elongation factor 2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / SERPINE1 mRNA-binding protein 1 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsAnger AM / Armache J-P / Berninghausen O / Habeck M / Subklewe M / Wilson DN / Beckmann R
CitationJournal: Nature / Year: 2013
Title: Structures of the human and Drosophila 80S ribosome.
Authors: Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann /
Abstract: Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex ...Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.
History
DepositionFeb 28, 2013-
Header (metadata) releaseMay 1, 2013-
Map releaseMay 1, 2013-
UpdateJul 23, 2014-
Current statusJul 23, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v6x
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5592_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5592.map.gz / Format: CCP4 / Size: 66.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of H. sapiens 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.24 Å/pix.
x 261 pix.
= 322.987 Å		1.24 Å/pix.
x 250 pix.
= 309.375 Å		1.24 Å/pix.
x 274 pix.
= 339.075 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-0.77251107 - 3.07489705
Average (Standard dev.)0.08045188 (±0.2584852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-132-122-147
Dimensions250274261
Spacing274250261
CellA: 309.375 Å / B: 339.07498 Å / C: 322.9875 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2374980842912
M x/y/z250274261
origin x/y/z0.0000.0000.000
length x/y/z309.375339.075322.987
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S213
start NC/NR/NS-122-132-147
NC/NR/NS274250261
D min/max/mean-0.7733.0750.080

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Supplemental data

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Sample components

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Entire : Human 80S ribosome from PBMCs

EntireName: Human 80S ribosome from PBMCs
Components
  • Sample: Human 80S ribosome from PBMCs
  • Complex: 80S ribosome

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Supramolecule #1000: Human 80S ribosome from PBMCs

SupramoleculeName: Human 80S ribosome from PBMCs / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 4.5 MDa / Theoretical: 4.5 MDa

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Homo sapiens (human) / Strain: Armache & Anger (AA) PBMCs / synonym: human / Tissue: Blood
Molecular weightExperimental: 4.5 MDa / Theoretical: 4.5 MDa

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: Before plunging, blot for 3 seconds using two layers of filter paper.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateFeb 6, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 30000 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 90000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 90000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using an automatic selection program.
CTF correctionDetails: each subvolume
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 343343

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