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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 20
  • (60S ribosomal protein ...) x 17
  • (Large ribosomal subunit protein ...) x 22
  • (Ribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 10
  • (tRNA) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ubiquitin-like protein fubi and ribosomal protein S30
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • mRNA
KeywordsRIBOSOME / naked mole-rat / 80S
Function / homology
Function and homology information


gastrulation / protein-RNA complex assembly / protein-synthesizing GTPase / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of DNA-templated transcription initiation / negative regulation of DNA repair / supercoiled DNA binding ...gastrulation / protein-RNA complex assembly / protein-synthesizing GTPase / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of DNA-templated transcription initiation / negative regulation of DNA repair / supercoiled DNA binding / oxidized purine DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / laminin receptor activity / protein-DNA complex disassembly / protein kinase A binding / TOR signaling / protein localization to nucleus / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein targeting / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / spindle assembly / positive regulation of microtubule polymerization / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of cell cycle / translation regulator activity / ribosomal small subunit export from nucleus / negative regulation of protein ubiquitination / rough endoplasmic reticulum / laminin binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / MDM2/MDM4 family protein binding / Hsp70 protein binding / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / bone development / mRNA 3'-UTR binding / small-subunit processome / Hsp90 protein binding / positive regulation of non-canonical NF-kappaB signal transduction / response to virus / base-excision repair / kinase activity / mitotic spindle / ribosome biogenesis / ruffle membrane / cytoplasmic ribonucleoprotein granule / mRNA 5'-UTR binding / innate immune response in mucosa / transcription coactivator binding / rRNA processing / cellular response to hydrogen peroxide / cytosolic ribosome / cell differentiation / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / small ribosomal subunit rRNA binding / 5S rRNA binding / cell body / ribosomal large subunit assembly / small ribosomal subunit / DNA-binding transcription activator activity, RNA polymerase II-specific / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / antibacterial humoral response / DNA-binding transcription factor binding / microtubule binding / cytosolic large ribosomal subunit / : / cytoplasmic translation / defense response to Gram-positive bacterium / postsynaptic density / protein stabilization / rRNA binding / negative regulation of translation / mitochondrial inner membrane / apoptotic process / ribonucleoprotein complex / positive regulation of apoptotic process / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / mRNA binding / ubiquitin protein ligase binding / centrosome / positive regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleolus / dendrite / protein kinase binding
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / 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 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L13e / Ribosomal L38e protein family / Ribosomal protein S21e / Ribosomal protein L38e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal L40e family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / : / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S7e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S17e, conserved site / Ribosomal protein L40e superfamily / Ribosomal protein S17e signature. / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L30e signature 2. / Ribosomal protein S3, eukaryotic/archaeal
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL38 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S6 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL33 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL20 / 40S ribosomal protein S4 / Large ribosomal subunit protein uL22 / Ribosomal protein L37 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L7a / 60S ribosomal protein L37a / 40S ribosomal protein S26 / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S29 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S23 / 60S ribosomal protein L13 / 40S ribosomal protein S24 / 40S ribosomal protein S18 / Large ribosomal subunit protein uL29 / 60S ribosomal protein L27a / 40S ribosomal protein S13 / Ubiquitin-like protein fubi and ribosomal protein S30 / 40S ribosomal protein S17 / 40S ribosomal protein S15a isoform X1 / 40S ribosomal protein S25 / 60S ribosomal protein L15 / Large ribosomal subunit protein uL23 / 60S ribosomal protein L26 / 60S ribosomal protein L24 / 40S ribosomal protein S16 / 60S ribosomal protein L23 / 60S ribosomal protein L36 / 60S ribosomal protein L34 / 60S ribosomal protein L13a isoform X1 / 40S ribosomal protein S9 / 40S ribosomal protein S15 / 60S ribosomal protein L32 / 40S ribosomal protein S20 / 40S ribosomal protein S19 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L10 / 40S ribosomal protein S8 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS7 / 60S ribosomal protein L18 / Large ribosomal subunit protein eL30 / 60S ribosomal protein L27 / Ribosomal protein L19 / Large ribosomal subunit protein eL28 / 60S ribosomal protein L36a / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL6 / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S21
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: Nat Commun / Year: 2026
Title: Cryo-EM structure of the naked mole-rat ribosome reveals a stabilized split 28S rRNA.
Authors: Mehmet Gül / Alice Rossi / Christian M T Spahn / Gary R Lewin / Mikhail Kudryashev /
Abstract: The naked mole-rat (Heterocephalus glaber) is a long-lived mammal with resistance to cancer and hypoxia, suggesting the evolution of robust proteostasis networks. The ribosome, central for protein ...The naked mole-rat (Heterocephalus glaber) is a long-lived mammal with resistance to cancer and hypoxia, suggesting the evolution of robust proteostasis networks. The ribosome, central for protein synthesis, is key to cellular stress responses and has an unusual feature: the 28S rRNA split; however, the details of its organization remain unknown. Here, we present high-resolution cryo-EM structures of the naked mole-rat 80S ribosome in four states of the elongation cycle. The structures reveal a conserved overall architecture and rRNA modification landscape compared to other mammals, and provide an atomic-level view of the distinct break in the 28S rRNA. This cleavage event, located in the D6 expansion segment, is structurally stabilized by a network of interactions with surrounding ribosomal proteins, maintaining the integrity of the large subunit. Our comparative analysis revealed that this compensatory network preserves a canonical architecture that is nearly indistinguishable from intact mouse and human ribosomes. These findings resolve the structural basis of this distinct cleavage, showing that it is a stable, integrated feature whose function is likely linked to more subtle regulatory mechanisms, rather than inducing major structural rearrangements.
History
DepositionNov 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2026Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession

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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: 60S ribosomal protein L7a
LH: Large ribosomal subunit protein uL6
LI: 60S ribosomal protein L10
LJ: Large ribosomal subunit protein uL5
LL: 60S ribosomal protein L13
LM: Large ribosomal subunit protein eL14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a isoform X1
LP: Large ribosomal subunit protein uL22
LQ: 60S ribosomal protein L18
LR: Ribosomal protein L19
LS: Large ribosomal subunit protein eL20
LT: Large ribosomal subunit protein eL21
LU: Large ribosomal subunit protein eL22
LV: 60S ribosomal protein L23
LW: 60S ribosomal protein L24
LX: Large ribosomal subunit protein uL23
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
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: 60S ribosomal protein L34
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: 60S ribosomal protein L37a
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: 40S ribosomal protein S4
SF: Small ribosomal subunit protein uS7
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein S9
SK: Small ribosomal subunit protein eS10
SL: Small ribosomal subunit protein uS17
SN: 40S ribosomal protein S13
SO: Small ribosomal subunit protein uS11
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SW: 40S ribosomal protein S15a isoform X1
SX: 40S ribosomal protein S23
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: 40S ribosomal protein S27
Sc: Small ribosomal subunit protein eS28
Sd: 40S ribosomal protein S29
Se: Ubiquitin-like protein fubi and ribosomal protein S30
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 ... , 22 types, 22 molecules LALCLDLELFLHLJLMLPLSLTLULXLbLcLdLfLhLkLlLrLB

#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


Mass: 47259.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#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: A0AAX6P0W2
#8: Protein Large ribosomal subunit protein eL6


Mass: 33593.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#9: Protein Large ribosomal subunit protein uL30


Mass: 31492.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#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: G5C3U8
#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
#15: Protein Large ribosomal subunit protein eL14


Mass: 23620.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#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
#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: A0A0P6JCV6
#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: G5ATV5
#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
#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: A0AAX6PQW7
#30: Protein Large ribosomal subunit protein eL29


Mass: 17635.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#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: G5BJ16
#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
#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: A0AAX6PDT5
#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: A0A0P6IYP5
#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
#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: G5BVZ2
#80: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3


Mass: 46212.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6IYN5

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60S ribosomal protein ... , 17 types, 17 molecules LGLILLLNLOLQLVLWLYLZLaLeLgLiLnLoLp

#10: Protein 60S ribosomal protein L7a


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6K8Y4
#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
#14: Protein 60S ribosomal protein L13


Mass: 24364.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6P3F5
#16: Protein 60S 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: A0AAX6PQU7
#17: Protein 60S ribosomal protein L13a isoform X1


Mass: 23519.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6Q4S4
#19: Protein 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: G5B890
#24: Protein 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: A0AAX6PVG0
#25: Protein 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: A0AAX6PSU9
#27: Protein 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: A0AAX6PRM3
#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
#29: Protein 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: A0AAX6PG51
#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: A0AAX6QD41
#35: Protein 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: A0AAX6Q439
#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: A0AAX6Q2T6
#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


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
#44: Protein 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: A0AAX6NNU1

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Ribosomal protein ... , 2 types, 2 molecules LRLj

#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 protein fubi 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: A0AAX6PHM7

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Small ribosomal subunit protein ... , 10 types, 10 molecules SASBSCSDSFSKSLSOScSg

#49: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32867.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6K1L6
#50: Protein Small ribosomal subunit protein eS1


Mass: 29942.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C1K3
#51: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6QEX7
#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: G5AS76, DNA-(apurinic or apyrimidinic site) lyase
#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: G5B7K7
#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: A0A0P6IZJ7
#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
#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: A0A0N8ESF7
#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: G5B4M2
#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 ... , 20 types, 20 molecules SESGSHSISJSNSPSQSRSSSTSUSVSWSXSYSZSaSbSd

#53: Protein 40S ribosomal protein S4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JF61
#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: A0AAX6NNW6, protein-synthesizing GTPase
#57: Protein 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: G5ARV4
#58: Protein 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: A0AAX6Q606
#61: Protein 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: A0AAX6PGK5
#63: Protein 40S ribosomal protein S15


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6Q6L0
#64: Protein 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: A0AAX6PUA9
#65: Protein 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: A0AAX6PIW5
#66: Protein 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: A0AAX6PA22
#67: Protein 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: A0AAX6QEV3
#68: Protein 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: A0AAX6QEN2
#69: Protein 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: G5C8F1
#70: Protein 40S ribosomal protein S15a isoform X1


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6PNI7
#71: Protein 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: A0AAX6P1S3
#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
#73: Protein 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: A0AAX6PPX8
#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: A0AAX6NNU4
#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: A0AAX6NNV5
#77: Protein 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: A0AAX6NS13

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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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