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- PDB-9kdu: Cryo-EM structure of 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 9kdu
TitleCryo-EM structure of 80S ribosome
Components
  • (Large ribosomal subunit protein ...) x 40
  • (Mus musculus ...) x 4
  • (Small ribosomal subunit protein ...) x 31
  • Nascent peptide
  • P tRNA
  • RNA (5'-R(P*AP*UP*CP*AP*UP*GP*AP*AP*GP*U)-3')
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
  • Ubiquitin-ribosomal protein eL40 fusion protein
KeywordsRIBOSOME / Native 80S 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 / 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 / Protein methylation / TCF dependent signaling in response to WNT / 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 / Regulation of FZD by ubiquitination
Similarity search - Function
40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-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 / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-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 / 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 S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / 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 L13e / Ribosomal protein L13e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e, conserved site / 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 / 40S Ribosomal protein S10 / 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 L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal L40e family / Ribosomal protein S25 / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / : / Ribosomal protein L36e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S7e signature. / 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 L40e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / :
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 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 eS10 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL16-like / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL39-like / 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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLu, Y. / Wang, X. / Qin, Y. / Cao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468 China
CitationJournal: To Be Published
Title: Cryo-EM structure of 80S ribosome
Authors: Lu, Y. / Wang, X. / Qin, Y. / Cao, Y.
History
DepositionNov 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L5: Mus musculus 28S ribosomal RNA
L7: Mus musculus 5S ribosomal RNA
L8: Mus musculus 5.8S ribosomal RNA
LA: Large ribosomal subunit protein uL2
LB: Large ribosomal subunit protein uL3
LC: Large ribosomal subunit protein uL4
LD: Large ribosomal subunit protein uL18
LE: Large ribosomal subunit protein eL6
LF: Large ribosomal subunit protein uL30
LG: Large ribosomal subunit protein eL8
LH: Large ribosomal subunit protein uL6
LI: Large ribosomal subunit protein uL16-like
LJ: Large ribosomal subunit protein uL5
LL: Large ribosomal subunit protein eL13
LM: Large ribosomal subunit protein eL14
LN: Large ribosomal subunit protein eL15
LO: Large ribosomal subunit protein uL13
LP: Large ribosomal subunit protein uL22
LQ: Large ribosomal subunit protein eL18
LR: Large ribosomal subunit protein eL19
LS: Large ribosomal subunit protein eL20
LT: Large ribosomal subunit protein eL21
LU: Large ribosomal subunit protein eL22
LV: Large ribosomal subunit protein uL14
LW: Large ribosomal subunit protein eL24
LX: Large ribosomal subunit protein uL23
LY: Large ribosomal subunit protein uL24
LZ: Large ribosomal subunit protein eL27
La: Large ribosomal subunit protein uL15
Lb: Large ribosomal subunit protein eL29
Lc: Large ribosomal subunit protein eL30
Ld: Large ribosomal subunit protein eL31
Le: Large ribosomal subunit protein eL32
Lf: Large ribosomal subunit protein eL33
Lg: Large ribosomal subunit protein eL34
Lh: Large ribosomal subunit protein uL29
Li: Large ribosomal subunit protein eL36
Lj: Large ribosomal subunit protein eL37
Lk: Large ribosomal subunit protein eL38
Ll: Large ribosomal subunit protein eL39-like
Lm: Ubiquitin-ribosomal protein eL40 fusion protein
Ln: Small ribosomal subunit protein eS32
Lo: Large ribosomal subunit protein eL42
Lp: Large ribosomal subunit protein eL43
Lr: Large ribosomal subunit protein eL28
S2: Mus musculus 18S ribosomal RNA
S7: P tRNA
SA: Small ribosomal subunit protein uS2
SB: Small ribosomal subunit protein eS1
SC: Small ribosomal subunit protein uS5
SD: Small ribosomal subunit protein uS3
SE: Small ribosomal subunit protein eS4
SF: Small ribosomal subunit protein uS7
SG: Small ribosomal subunit protein eS6
SH: Small ribosomal subunit protein eS7
SI: Small ribosomal subunit protein eS8
SJ: Small ribosomal subunit protein uS4
SK: Small ribosomal subunit protein eS10
SL: Small ribosomal subunit protein uS17
SN: Small ribosomal subunit protein uS15
SO: Small ribosomal subunit protein uS11
SP: Small ribosomal subunit protein uS19
SQ: Small ribosomal subunit protein uS9
SR: Small ribosomal subunit protein eS17
SS: Small ribosomal subunit protein uS13
ST: Small ribosomal subunit protein eS19
SU: Small ribosomal subunit protein uS10
SV: Small ribosomal subunit protein eS21
SW: Small ribosomal subunit protein uS8
SX: Small ribosomal subunit protein uS12
SY: Small ribosomal subunit protein eS24
SZ: Small ribosomal subunit protein eS25
Sa: Small ribosomal subunit protein eS26
Sb: Small ribosomal subunit protein eS27
Sc: Small ribosomal subunit protein eS28
Sd: Small ribosomal subunit protein uS14
Se: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Sg: Small ribosomal subunit protein RACK1
Sx: RNA (5'-R(P*AP*UP*CP*AP*UP*GP*AP*AP*GP*U)-3')
Z: Nascent peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,679,277180
Polymers3,676,72380
Non-polymers2,554100
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Mus musculus ... , 4 types, 4 molecules L5L7L8S2

#1: RNA chain Mus musculus 28S ribosomal RNA


Mass: 1530907.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: RNA chain Mus musculus 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 2589141237
#3: RNA chain Mus musculus 5.8S ribosomal RNA


Mass: 50795.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#46: RNA chain Mus musculus 18S ribosomal RNA


Mass: 603101.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Large ribosomal subunit protein ... , 40 types, 40 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

#4: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62918
#5: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / J1 protein


Mass: 46212.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P27659
#6: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 47259.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8E6
#7: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34464.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47962
#8: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / TAX-responsive enhancer element-binding protein 107 / TAXREB107


Mass: 33593.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47911
#9: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 31492.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14148
#10: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / Surfeit locus protein 3


Mass: 30042.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12970
#11: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21917.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51410
#12: Protein Large ribosomal subunit protein uL16-like / 60S ribosomal protein L10-like


Mass: 24612.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P86048
#13: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXW4
#14: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / A52


Mass: 24364.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47963
#15: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 23620.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR57
#16: Protein Large ribosomal subunit protein eL15 / 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZM2
#17: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / Transplantation antigen P198 / Tum-P198 antigen


Mass: 23519.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19253
#18: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPR4
#19: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21698.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35980
#20: Protein Large ribosomal subunit protein eL19 / 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84099
#21: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20778.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62717
#22: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18624.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09167
#23: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / Heparin-binding protein HBp15


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P67984
#24: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62830
#25: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BP67
#26: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62751
#27: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26 / Silica-induced gene 20 protein / SIG-20


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61255
#28: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61358
#29: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a / L29


Mass: 16648.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14115
#30: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29


Mass: 17635.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47915
#31: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62889
#32: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62900
#33: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62911
#34: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O55142
#35: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13325.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1R9
#36: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14595.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV7
#37: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47964
#38: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D823
#39: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8224.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JJI8
#40: Protein Large ribosomal subunit protein eL39-like / 60S ribosomal protein L39-like


Mass: 6355.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQD0
#43: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P83882
#44: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61514
#45: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 15770.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P41105

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Protein , 2 types, 2 molecules LmSe

#41: Protein Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62984
#77: Protein Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / FAU ubiquitin-like and ribosomal protein S30


Mass: 14441.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62862

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Small ribosomal subunit protein ... , 31 types, 31 molecules LnSASBSCSDSESFSGSHSISJSKSLSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSg

#42: Protein/peptide Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62947
#48: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / ...37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / OFA/iLRP


Mass: 32867.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14206
#49: Protein Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a / Protein TU-11


Mass: 29942.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97351
#50: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25444
#51: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P62908, DNA-(apurinic or apyrimidinic site) lyase
#52: Protein Small ribosomal subunit protein eS4 / 40S ribosomal protein S4 / X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62702
#53: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97461
#54: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6 / Phosphoprotein NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62754
#55: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62082
#56: Protein Small ribosomal subunit protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62242
#57: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWN5
#58: Protein Small ribosomal subunit protein eS10 / 40S ribosomal protein S10


Mass: 18951.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63325
#59: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62281
#60: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62301
#61: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62264
#62: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62843
#63: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14131
#64: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63276
#65: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62270
#66: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16117.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZX8
#67: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P60867
#68: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9154.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQR2
#69: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62245
#70: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62267
#71: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62849
#72: Protein Small ribosomal subunit protein eS25 / 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62852
#73: Protein Small ribosomal subunit protein eS26 / 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62855
#74: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWU9
#75: Protein Small ribosomal subunit protein eS28 / 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62858
#76: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62274
#78: Protein Small ribosomal subunit protein RACK1 / 12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / ...12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated protein kinase C 1 / p205


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68040

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RNA chain , 2 types, 2 molecules S7Sx

#47: RNA chain P tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#79: RNA chain RNA (5'-R(P*AP*UP*CP*AP*UP*GP*AP*AP*GP*U)-3')


Mass: 3185.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein/peptide , 1 types, 1 molecules Z

#80: Protein/peptide Nascent peptide


Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 2 types, 100 molecules

#81: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 97 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#82: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Cryo EM structure of 80s ribosome / Type: RIBOSOME / Entity ID: #1-#80 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38804 / Symmetry type: POINT

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