- EMDB-53262: Mouse Ribosome POST translocation state -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-53262
Title
Mouse Ribosome POST translocation state
Map data
Sample
Complex: Elogating Ribosome in POST translocation state
Protein or peptide: x 76 types
RNA: x 3 types
Protein or peptide: x 1 types
RNA: x 3 types
Ligand: x 3 types
Keywords
Translating Ribosomes / POST state / Mouse / Ba/F3 / Polysomes / RIBOSOME
Function / homology
Function and homology information
TNFR1-mediated ceramide production / 5.8S rRNA binding / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex ...TNFR1-mediated ceramide production / 5.8S rRNA binding / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / negative regulation of protein neddylation / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / Regulation of pyruvate metabolism / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Formation of a pool of free 40S subunits / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / SRP-dependent cotranslational protein targeting to membrane / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Major pathway of rRNA processing in the nucleolus and cytosol / E3 ubiquitin ligases ubiquitinate target proteins / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Dual incision in TC-NER / Oncogene Induced Senescence / Degradation of CRY and PER proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of BACH1 activity / TNFR1-induced NF-kappa-B signaling pathway / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / Protein methylation / PINK1-PRKN Mediated Mitophagy / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Inactivation of CSF3 (G-CSF) signaling Similarity search - Function
40S ribosomal protein SA / Ribosomal protein L6, N-terminal / 40S ribosomal protein SA, C-terminal domain / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : ...40S ribosomal protein SA / Ribosomal protein L6, N-terminal / 40S ribosomal protein SA, C-terminal domain / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / S27a-like superfamily / Ribosomal protein L10e, conserved site / : / Ribosomal protein L10e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 40S Ribosomal protein S10 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / : / : / Ribosomal protein S27a / Ribosomal L40e family / Ribosomal protein S27a / Ribosomal protein S7e signature. / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S25 / S25 ribosomal protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site Similarity search - Domain/homology
Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL3 ...Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL20 / 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 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 Similarity search - Component
Biological species
Mus musculus (house mouse)
Method
single particle reconstruction / cryo EM / Resolution: 2.78 Å
Entire : Elogating Ribosome in POST translocation state
Entire
Name: Elogating Ribosome in POST translocation state
Components
Complex: Elogating Ribosome in POST translocation state
Protein or peptide: Large ribosomal subunit protein uL30
Protein or peptide: Small ribosomal subunit protein uS13
Protein or peptide: Large ribosomal subunit protein eL8
RNA: 5S ribosomal RNA
Protein or peptide: Small ribosomal subunit protein eS19
RNA: transfer RNA
Protein or peptide: Large ribosomal subunit protein uL6
RNA: 5.8S ribosomal RNA
Protein or peptide: Small ribosomal subunit protein uS10
Protein or peptide: Large ribosomal subunit protein uL16
Protein or peptide: Large ribosomal subunit protein uL2
Protein or peptide: Small ribosomal subunit protein eS21
Protein or peptide: Large ribosomal subunit protein uL5
Protein or peptide: Large ribosomal subunit protein uL3
Protein or peptide: Small ribosomal subunit protein uS12
Protein or peptide: Large ribosomal subunit protein eL13
Protein or peptide: Large ribosomal subunit protein uL4
Protein or peptide: Small ribosomal subunit protein eS26
Protein or peptide: Large ribosomal subunit protein eL14
Protein or peptide: Large ribosomal subunit protein uL18
Protein or peptide: Small ribosomal subunit protein eS28
Protein or peptide: Large ribosomal subunit protein eL15
Protein or peptide: Large ribosomal subunit protein eL6
Protein or peptide: Small ribosomal subunit protein uS14
Protein or peptide: Large ribosomal subunit protein uL13
Protein or peptide: Small ribosomal subunit protein RACK1
Protein or peptide: Large ribosomal subunit protein uL22
Protein or peptide: Small ribosomal subunit protein uS5
Protein or peptide: Large ribosomal subunit protein eL18
Protein or peptide: Small ribosomal subunit protein eS6
Protein or peptide: Large ribosomal subunit protein uL1
Protein or peptide: Large ribosomal subunit protein eL19
Protein or peptide: Small ribosomal subunit protein uS4
Protein or peptide: Large ribosomal subunit protein eL20
Protein or peptide: Small ribosomal subunit protein eS12
Protein or peptide: Large ribosomal subunit protein eL21
Protein or peptide: Small ribosomal subunit protein uS15
Protein or peptide: Large ribosomal subunit protein eL22
Protein or peptide: Small ribosomal subunit protein uS11
Protein or peptide: Large ribosomal subunit protein uL14
Protein or peptide: Small ribosomal subunit protein uS8
Protein or peptide: Large ribosomal subunit protein eL24
Protein or peptide: Small ribosomal subunit protein eS24
Protein or peptide: Large ribosomal subunit protein uL23
Protein or peptide: Small ribosomal subunit protein eS25
Protein or peptide: Large ribosomal subunit protein uL24
Protein or peptide: Small ribosomal subunit protein eS27
Protein or peptide: Large ribosomal subunit protein eL27
Protein or peptide: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Protein or peptide: Large ribosomal subunit protein uL15
Protein or peptide: Ubiquitin-ribosomal protein eS31 fusion protein
Protein or peptide: Large ribosomal subunit protein eL29
Protein or peptide: Large ribosomal subunit protein eL30
Protein or peptide: Large ribosomal subunit protein eL31
Protein or peptide: Large ribosomal subunit protein eL32
Protein or peptide: Large ribosomal subunit protein eL33
Protein or peptide: Large ribosomal subunit protein eL34
Protein or peptide: Large ribosomal subunit protein uL29
Protein or peptide: Large ribosomal subunit protein eL36
Protein or peptide: Large ribosomal subunit protein eL37
Protein or peptide: Large ribosomal subunit protein eL38
Protein or peptide: Large ribosomal subunit protein eL39
Protein or peptide: Ubiquitin-ribosomal protein eL40 fusion protein
Protein or peptide: 60S ribosomal protein L41
Protein or peptide: Large ribosomal subunit protein eL42
Protein or peptide: Large ribosomal subunit protein eL43
Protein or peptide: Large ribosomal subunit protein eL28
Protein or peptide: Small ribosomal subunit protein uS2
Protein or peptide: 40S ribosomal protein S3a
Protein or peptide: Small ribosomal subunit protein uS3
Protein or peptide: Small ribosomal subunit protein eS4
Protein or peptide: Small ribosomal subunit protein uS7
Protein or peptide: Small ribosomal subunit protein eS7
Protein or peptide: Small ribosomal subunit protein eS8
Protein or peptide: Small ribosomal subunit protein eS10
Protein or peptide: Small ribosomal subunit protein uS17
Protein or peptide: Small ribosomal subunit protein uS19
Protein or peptide: Small ribosomal subunit protein uS9
Protein or peptide: Small ribosomal subunit protein eS17
Protein or peptide: Nascent protein chain
RNA: 28S ribosomal RNA
RNA: messenger RNA
RNA: 18S ribosomal RNA
Ligand: MAGNESIUM ION
Ligand: ZINC ION
Ligand: water
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Supramolecule #1: Elogating Ribosome in POST translocation state
Supramolecule
Name: Elogating Ribosome in POST translocation state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#7, #9-#69, #71-#82 Details: de-novo peptide chain By is only visible in the Refine 3D map
Details: 20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT
Grid
Model: Quantifoil Active R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0003 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP
Details
RNA concentration was measured by nanordrop
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Electron microscopy
Microscope
FEI TALOS ARCTICA
Image recording
Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 7139 / Average electron dose: 45.0 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
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