EMDB-18169: Composite map of the Gallus gallus 80S rotated ribosome in comple...

Basic information

Entry

Database: EMDB / ID: EMD-18169

• Title: Composite map of the Gallus gallus 80S rotated ribosome in complex with eEF2 and SERBP1
• Map data: Composite map of the Gallus gallus 80S rotated ribosome in complex with eEF2 and SERBP1

Sample

• Complex: 80S Gallus gallus ribosome from chicken embryo

• Keywords: translation / complex / eEF2 / SERBP1 / RIBOSOME

Function / homology

Function:

TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / 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) / Regulation of PLK1 Activity at G2/M Transition / 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) / 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 / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / 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 / ER Quality Control Compartment (ERQC) / NOTCH3 Activation and Transmission of Signal to the Nucleus / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT)

Domain/homology:

: / Glycerate/sugar phosphate transporter, conserved site / glpT family of transporters signature. / 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 / Major facilitator superfamily / Major Facilitator Superfamily / : / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L2, archaeal-type / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Ribosomal protein L30e / 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 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / 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. / : / Ribosomal protein S26e signature. / MFS transporter superfamily / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L14e domain / Ribosomal protein L1, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L1 signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L1 / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal protein L14 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / : / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature.

Component:

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 eL42 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS14 / SERPINE1 mRNA binding protein 1 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL11 / 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 / Large ribosomal subunit protein uL24 / Ribosomal protein / 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 / Large ribosomal subunit protein uL10 / 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 / Small ribosomal subunit protein uS11 / 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 / Elongation factor 2 / 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 / 40S ribosomal protein S16 / 60S ribosomal protein L21

• Biological species: Gallus gallus (chicken)
• Method: single particle reconstruction / cryo EM / Resolution: 2.4 Å
• Authors: Nurullina L / Jenner L / Myasnikov A / Yusupov M

Funding support

France, 1 items

Organization	Grant number	Country
Fondation pour la Recherche Medicale (FRM)		France

• Citation: Journal: To Be Published; Title: Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells; Authors: Nurullina L / Terrosu S / Jenner L / Myasnikov A / Yusupov M

History

Deposition	Aug 8, 2023	-
Header (metadata) release	Aug 21, 2024	-
Map release	Aug 21, 2024	-
Update	Aug 21, 2024	-
Current status	Aug 21, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_18169.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Composite map of the Gallus gallus 80S rotated ribosome in complex with eEF2 and SERBP1
• Voxel size: X=Y=Z: 0.803 Å

Density

Contour Level	By AUTHOR: 3.0
Minimum - Maximum	-17.913443000000001 - 35.597855000000003
Average (Standard dev.)	-0.001120761 (±1.0801704)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 580 580 580 Spacing 580 580 580
Cell	A=B=C: 465.74 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : 80S Gallus gallus ribosome from chicken embryo

• Entire: Name: 80S Gallus gallus ribosome from chicken embryo

Components

• Complex: 80S Gallus gallus ribosome from chicken embryo

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

• Supramolecule: Name: 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, eEF2, SERBP1
• Source (natural): Organism: Gallus gallus (chicken) / Tissue: embryo
• Molecular weight: Theoretical: 4.3 MDa

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Energy filter - Name: TFS Selectris X
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 32439 / Average electron dose: 40.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination 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 stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 641721

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

7o7z

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Details: Composite map / Number images used: 100204
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

Atomic model buiding 1

Initial model

PDB ID:

7o7z

Chain - Source name: PDB / Chain - Initial model type: experimental model

• Refinement: Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

Output model

PDB-8q87:
Structure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1