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- EMDB-5591: Electron cryo-microscopy of Drosophila melanogaster EF2- and Vig2... -

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Basic information

Entry
Database: EMDB / ID: EMD-5591
TitleElectron cryo-microscopy of Drosophila melanogaster EF2- and Vig2-bound 80S ribosome
Map dataReconstruction of D. melanogaster 80S ribosome
Sample
  • Sample: 80S D. melanogaster ribosome
  • Complex: 80S ribosome with E-tRNA, EF-2, and Vig2
Keywordseukarya eukaryotic ribosomal ribosome 80S protein RNA cryo-electron microscopy protein synthesis mass spectrometry drosophila
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / : / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / TCF dependent signaling in response to WNT / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / : / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / TCF dependent signaling in response to WNT / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of PLK1 Activity at G2/M Transition / Regulation of innate immune responses to cytosolic DNA / RMTs methylate histone arginines / Regulation of TNFR1 signaling / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of TP53 Degradation / Cyclin D associated events in G1 / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / GTP hydrolysis and joining of the 60S ribosomal subunit / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Protein methylation / ER Quality Control Compartment (ERQC) / Iron uptake and transport / RAS processing / Pexophagy / Regulation of BACH1 activity / polytene chromosome chromocenter / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translesion synthesis by POLK / Translesion synthesis by POLI / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Formation of TC-NER Pre-Incision Complex / Peroxisomal protein import / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC-Cdc20 mediated degradation of Nek2A / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Downstream TCR signaling / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Degradation of AXIN / Degradation of DVL / PINK1-PRKN Mediated Mitophagy / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Negative regulation of MAPK pathway / NIK-->noncanonical NF-kB signaling / Josephin domain DUBs / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / KEAP1-NFE2L2 pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Nuclear CI is degraded / ABC-family proteins mediated transport / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / Dual Incision in GG-NER / Dual incision in TC-NER / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK1 recruits IKK complex / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Ubiquitination and proteolysis of phosphorylated CI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Spry regulation of FGF signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling
Similarity search - Function
: / 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 / Ribosomal protein L28e / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...: / 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 / Ribosomal protein L28e / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal L28e/Mak16 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal L28e protein family / Ribosomal protein L30e / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / : / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / EF-G domain III/V-like / 60S ribosomal protein L10P, insertion domain / Small (40S) ribosomal subunit Asc1/RACK1 / Insertion domain in 60S ribosomal protein L10P / : / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Tr-type G domain, conserved site / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / metallochaperone-like domain / TRASH domain / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S19e, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein S21e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein L35Ae, conserved site / 40S Ribosomal protein S10 / Ribosomal_S17 N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal protein S7e
Similarity search - Domain/homology
Small ribosomal subunit protein uS11A / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL4 ...Small ribosomal subunit protein uS11A / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS26 / Eukaryotic translation elongation factor 2 / 40S ribosomal protein S14b / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS17 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS7A / 40S ribosomal protein S15 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS12 / 60S ribosomal protein L41 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL31 / 60S ribosomal protein L21 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein eS7 / 40S ribosomal protein S10a / 60S ribosomal protein L34 / 60S ribosomal protein L27 / 40S ribosomal protein S27 / Vig2, isoform B / 40S ribosomal protein S30 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL24 / IP17351p / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL28 / FI01658p / 60S ribosomal protein L12 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L35 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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: 0.49
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.49
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v6w
  • Surface level: 0.49
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5591_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5591.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of D. melanogaster 80S ribosome
Voxel sizeX=Y=Z: 1.2375 Å
Density
Contour LevelBy AUTHOR: 0.49 / Movie #1: 0.49
Minimum - Maximum-0.87690914 - 1.94252026
Average (Standard dev.)0.00273714 (±0.16781819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 455.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z455.400455.400455.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-0.8771.9430.003

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Supplemental data

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Sample components

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Entire : 80S D. melanogaster ribosome

EntireName: 80S D. melanogaster ribosome
Components
  • Sample: 80S D. melanogaster ribosome
  • Complex: 80S ribosome with E-tRNA, EF-2, and Vig2

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Supramolecule #1000: 80S D. melanogaster ribosome

SupramoleculeName: 80S D. melanogaster ribosome / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 4 MDa / Theoretical: 4 MDa

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Supramolecule #1: 80S ribosome with E-tRNA, EF-2, and Vig2

SupramoleculeName: 80S ribosome with E-tRNA, EF-2, and Vig2 / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly / Cell: embryo
Molecular weightExperimental: 4 MDa / Theoretical: 4 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 90000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 90000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateMar 10, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each subvolume
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 134500
DetailsThe particles were selected using an automatic selection program

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