- EMDB-53333: Mouse Ribosome rotated-1 PRE state -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-53333
Title
Mouse Ribosome rotated-1 PRE state
Map data
Sample
Complex: Elongating Ribosome in rotated-1 PRE
Protein or peptide: x 75 types
RNA: x 7 types
Ligand: x 3 types
Keywords
Translating Ribosomes / rotated-1 PRE state / Mouse / Ba/F3 / Polysomes / RIBOSOME
Function / homology
Function and homology information
TNFR1-mediated ceramide production / 5.8S rRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Protein hydroxylation / 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 / Formation of the ternary complex, and subsequently, the 43S complex / Protein hydroxylation / 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 / Stabilization of p53 / Formation of a pool of free 40S subunits / 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 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / E3 ubiquitin ligases ubiquitinate target proteins / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Dual incision in TC-NER / Oncogene Induced Senescence / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / TNFR1-induced NF-kappa-B signaling pathway / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / 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) / Regulation of BACH1 activity / EGFR downregulation / mammalian oogenesis stage / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / Protein methylation / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / PINK1-PRKN Mediated Mitophagy / Regulation of RUNX3 expression and activity Similarity search - Function
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 / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : ...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 / 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 / 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 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 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 S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L18/L18-A/B/e, conserved site / 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 S8e subdomain, eukaryotes / Ribosomal L40e family / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L36e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S17e, conserved site / Ribosomal protein L40e superfamily / Ribosomal protein S17e signature. / Ribosomal protein L27e 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 / 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 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: 3.4 Å
Protein or peptide: Large ribosomal subunit protein uL30
RNA: 28S ribosomal RNA
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
RNA: messenger RNA
Protein or peptide: Nascent protein chain
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 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: 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
RNA: 18S ribosomal RNA
RNA: transfer RNA
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
Ligand: MAGNESIUM ION
Ligand: ZINC ION
Ligand: water
+
Supramolecule #1: Elongating Ribosome in rotated-1 PRE
Supramolecule
Name: Elongating Ribosome in rotated-1 PRE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#82 Details: de-novo peptide chain By is only visible in the Refine 3D map
Source (natural)
Organism: Mus musculus (house mouse)
Molecular weight
Theoretical: 4.3 MDa
+
Macromolecule #1: Large ribosomal subunit protein uL30
Macromolecule
Name: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1mM DTT
Grid
Model: Quantifoil 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: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
Vitrification
Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP
Details
RNA concentration was measured by nanodrop
-
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
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi