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- PDB-9t5c: Naked mole-rat 80S ribosome in post-translocation non-rotated state -

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Basic information

Entry
Database: PDB / ID: 9t5c
TitleNaked mole-rat 80S ribosome in post-translocation non-rotated state
Components
  • (40S ribosomal protein ...) x 6
  • (60S ribosomal protein ...) x 6
  • (Large ribosomal subunit protein ...) x 32
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 24
  • (tRNA) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • mRNA
KeywordsRIBOSOME / naked mole-rat / 80S
Function / homology
Function and homology information


Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / SRP-dependent cotranslational protein targeting to membrane / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / 5.8S rRNA binding / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of protein neddylation / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Protein methylation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation at postsynapse / RMTs methylate histone arginines / A band / aminoacyl-tRNA synthetase multienzyme complex / translation at presynapse / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / 90S preribosome assembly / nucleolus organization / GAIT complex / TORC2 complex binding / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / cell-substrate adhesion / laminin receptor activity / homeostatic process / macrophage chemotaxis / lung morphogenesis / positive regulation of natural killer cell proliferation / basement membrane / fibroblast growth factor binding / monocyte chemotaxis / TOR signaling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / ubiquitin ligase inhibitor activity / 90S preribosome / ribonucleoprotein complex binding / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / regulation of translational fidelity / maturation of LSU-rRNA / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / Notch signaling pathway / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rough endoplasmic reticulum / positive regulation of cell cycle / laminin binding / ribosomal small subunit export from nucleus / gastrulation / translation initiation factor binding / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-4
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 L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e, conserved site / : / Ribosomal protein S19e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 40S Ribosomal protein S10 / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S25 / : / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature.
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S6 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL33 / 60S ribosomal protein L41 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL22 / Ribosomal protein L37 / Large ribosomal subunit protein eL39 / 40S ribosomal protein S24 / 60S ribosomal protein L10 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL43 / 40S ribosomal protein S26 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS8 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Ribosomal protein L15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL14 / 60S ribosomal protein L27 / Ribosomal protein L19 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L36a / 60S ribosomal protein L32 / Large ribosomal subunit protein eL24 / 60S ribosomal protein L36 / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL21 / 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 uL6 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL20 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38
Similarity search - Component
Biological speciesHeterocephalus glaber (naked mole-rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsGul, M. / Kudryashev, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU3222/3-1 Germany
CitationJournal: To Be Published
Title: Naked mole-rat 80S ribosome in post-translocation non-rotated state
Authors: Gul, M. / Kudryashev, M.
History
DepositionNov 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: mRNA
L5: 28S ribosomal RNA
L7: 5S ribosomal RNA
L8: 5.8S ribosomal RNA
LA: Large ribosomal subunit protein uL2
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: 60S ribosomal protein L10
LJ: Large ribosomal subunit protein uL5
LL: Large ribosomal subunit protein eL13
LM: Large ribosomal subunit protein eL14
LN: Ribosomal protein L15
LO: Large ribosomal subunit protein uL13
LP: Large ribosomal subunit protein uL22
LQ: Large ribosomal subunit protein eL18
LR: Ribosomal protein L19
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: 60S ribosomal protein L27
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: 60S ribosomal protein L32
Lf: Large ribosomal subunit protein eL33
Lg: Large ribosomal subunit protein eL34
Lh: Large ribosomal subunit protein uL29
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lk: Large ribosomal subunit protein eL38
Ll: Large ribosomal subunit protein eL39
Lm: Ubiquitin-ribosomal protein eL40 fusion protein
Ln: 60S ribosomal protein L41
Lo: 60S ribosomal protein L36a
Lp: Large ribosomal subunit protein eL43
Lr: Large ribosomal subunit protein eL28
S2: 18S ribosomal RNA
S6: tRNA
S7: 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: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
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: 40S ribosomal protein S15
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: 40S ribosomal protein S24
SZ: Small ribosomal subunit protein eS25
Sa: 40S ribosomal protein S26
Sb: 40S ribosomal protein S27
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
LB: Large ribosomal subunit protein uL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,708,321411
Polymers3,700,15380
Non-polymers8,168331
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 7 types, 7 molecules BL5L7L8S2S6S7

#1: RNA chain mRNA


Mass: 3108.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#2: RNA chain 28S ribosomal RNA


Mass: 1531040.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#3: RNA chain 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#4: RNA chain 5.8S ribosomal RNA


Mass: 50795.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#46: RNA chain 18S ribosomal RNA


Mass: 603062.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#47: RNA chain tRNA


Mass: 24128.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#48: RNA chain tRNA


Mass: 24082.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)

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Large ribosomal subunit protein ... , 32 types, 32 molecules LALCLDLELFLGLHLJLLLMLOLPLQLSLTLULVLWLXLYLaLbLcLdLfLgLhLkLlLpLrLB

#5: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J3A4
#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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P14148
#10: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: P62424
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P51410
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6IWW8
#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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q9CR57
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P19253
#18: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21421.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JH89
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P35980
#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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: O09167
#23: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0N8ESF8
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BK67
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C020
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q24JY1
#27: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B5G0
#29: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a


Mass: 16648.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BUW4
#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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q3T0D5
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0N8ESF6
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J939
#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) Heterocephalus glaber (naked mole-rat) / 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q6ZWV7
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q9JJI8
#40: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6NYH3
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: E3VX70
#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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P41105
#80: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P27659

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60S ribosomal protein ... , 6 types, 6 molecules LILZLeLiLnLo

#12: Protein 60S ribosomal protein L10


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6QHL6
#28: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BN91
#33: Protein 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BYD8
#37: Protein 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C0Q6
#42: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J950
#43: Protein 60S ribosomal protein L36a / 60S ribosomal protein L36a-like


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BW65

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Ribosomal protein ... , 3 types, 3 molecules LNLRLj

#16: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BFP9
#20: Protein Ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BRW3
#38: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JT91

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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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C5A6
#78: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P62862

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Small ribosomal subunit protein ... , 24 types, 24 molecules SASBSCSDSESFSISJSKSLSNSOSQSRSSSTSUSVSWSXSZScSdSg

#49: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P14206
#50: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P97351
#51: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P25444
#52: 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) Heterocephalus glaber (naked mole-rat)
References: UniProt: E2RH47, DNA-(apurinic or apyrimidinic site) lyase
#53: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q76N24
#54: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P97461
#57: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q5E958
#58: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22607.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5CBG2
#59: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P63325
#60: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J0Q6
#61: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B0I4
#62: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: P62265
#64: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BJD7
#65: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B1R5
#66: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0N8ESM4
#67: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q9CZX8
#68: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13331.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B335
#69: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9169.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q9CQR2
#70: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5AY31
#71: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15863.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J0V6
#73: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q56JX5
#76: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: Q56JX6
#77: 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) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JEN2
#79: Protein Small ribosomal subunit protein RACK1 / Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated ...Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated protein kinase C 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J231

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40S ribosomal protein ... , 6 types, 6 molecules SGSHSPSYSaSb

#55: Protein 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J125
#56: Protein 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C7L2
#63: Protein 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5AZL1
#72: Protein 40S ribosomal protein S24


Mass: 15449.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6PA11
#74: Protein 40S ribosomal protein S26


Mass: 13063.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: E3VX72
#75: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: E3VX74

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Non-polymers , 3 types, 337 molecules

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


Mass: 24.305 Da / Num. of mol.: 328 / Source method: obtained synthetically / Formula: Mg
#82: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#83: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 80S ribosome / Type: RIBOSOME / Entity ID: #1-#80 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Heterocephalus glaber (naked mole-rat)
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60.04 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
7PHENIXmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118185 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7CPU

7cpu


Accession code: 7CPU / Source name: PDB / Type: experimental model

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