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- EMDB-18168: Composite map of the Gallus gallus 80S non-rotated ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-18168
TitleComposite map of the Gallus gallus 80S non-rotated ribosome
Map dataComposite map of the Gallus gallus 80S non-rotated ribosome
Sample
  • Complex: 80S Gallus gallus ribosome from chicken embryo
Keywordstranslation / ribosome
Function / homology
Function and homology information


TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / : / glucose 6-phosphate:phosphate antiporter activity / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha ...TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / : / glucose 6-phosphate:phosphate antiporter activity / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / RAD18 and ubiquitinated PCNA-mediated recruitment of translesion polymerases / Nucleotide Excision Repair / Deactivation of the beta-catenin transactivating complex / TRAF6 mediated induction of proinflammatory cytokines / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NFkB activation mediated by RIP1 complexed with activated TLR3 / Activated TAK1 mediates p38 MAP kinase phosphorylation / Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / CLEC7A (Dectin-1) 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 / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / MAPK6/MAPK4 signaling / Josephin domain DUBs / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / NFkB and MAPK activation mediated by TRAF6 upon TLR7 or TLR21 stimulation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / Neddylation
Similarity search - Function
Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Ribosomal protein L14, KOW motif / 40S ribosomal protein SA / Major facilitator superfamily / Major Facilitator Superfamily / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal ...Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Ribosomal protein L14, KOW motif / 40S ribosomal protein SA / Major facilitator superfamily / Major Facilitator Superfamily / 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 / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / MFS transporter superfamily / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / 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. / 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 S8e subdomain, eukaryotes / Ribosomal protein L13e / 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 L44 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS8 ...Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL33 / Ribosomal protein L36a like / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L32 / Ribosomal protein S10 / Ribosomal protein L37 / 40S ribosomal protein S8 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL2 / 40S ribosomal protein S7 / DNA-(apurinic or apyrimidinic site) lyase / Ribosomal protein L15 / Ribosomal protein L26 like 1 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS13 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL13 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL30 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL28 / Ribosomal protein S14 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Ribosomal protein L19 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS9 / 60S ribosomal protein L21
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsNurullina L / Jenner L / Myasnikov A / Yusupov M
Funding support France, 1 items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: FEBS Lett / Year: 2024
Title: Cryo-EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold-stress conditions.
Authors: Liliia Nurullina / Salvatore Terrosu / Alexander G Myasnikov / Lasse Bohl Jenner / Marat Yusupov /
Abstract: Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor ...Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor eEF2 with GDP, SERPINE1 mRNA binding protein 1 (SERBP1) and deacylated tRNA in the P/E position, showing common features with complexes already described in mammals. Modeling of most expansion segments of G. gallus 28S ribosomal RNA allowed us to identify specific features in their structural organization and to describe areas where a marked difference between mammalian and avian ribosomes could shed light on the evolution of the expansion segments. This study provides the first structure of an avian ribosome, establishing a model for future structural and functional studies on the translational machinery in Aves.
History
DepositionAug 8, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18168.png

Downloads & links

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Map

FileDownload / File: emd_18168.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the Gallus gallus 80S non-rotated ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 580 pix.
= 465.74 Å		0.8 Å/pix.
x 580 pix.
= 465.74 Å		0.8 Å/pix.
x 580 pix.
= 465.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.803 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.28823045 - 2.8263237
Average (Standard dev.)0.021386107 (±0.063474275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 465.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 80S Gallus gallus ribosome from chicken embryo

EntireName: 80S Gallus gallus ribosome from chicken embryo
Components
  • Complex: 80S Gallus gallus ribosome from chicken embryo

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Supramolecule #1: 80S Gallus gallus ribosome from chicken embryo

SupramoleculeName: 80S Gallus gallus ribosome from chicken embryo / type: complex / ID: 1 / Parent: 0
Details: 28S rRNA, 5.8S rRNA, 5S rRNA, 18S rRNA,ribosomal proteins, tRNA
Source (natural)Organism: Gallus gallus (chicken) / Tissue: embryo
Molecular weightTheoretical: 4.3 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: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 32439 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 641721
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7o7z

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Details: Composite map / Number images used: 122598
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

7o7z


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient
Output model

PDB-8q7z:
Structure of the G. gallus 80S non-rotated ribosome

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