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- PDB-9y42: Structure of naked mole-rat ribosome with P/E tRNA and eEF2 (rotated) -

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Basic information

Entry
Database: PDB / ID: 9y42
TitleStructure of naked mole-rat ribosome with P/E tRNA and eEF2 (rotated)
Components
  • (40S ribosomal protein ...) x 17
  • (60S ribosomal protein ...) x 21
  • (Large ribosomal subunit protein ...) x 18
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 15
  • (Ubiquitin-ribosomal protein ...) x 2
  • 18S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • LSU alpha rRNA
  • LSU beta rRNA
  • P/E tRNA (77-MER)
  • eEF2
KeywordsRIBOSOME / Naked mole rat ribosome
Function / homology
Function and homology information


regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of DNA repair / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex ...regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of DNA repair / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / neural crest cell differentiation / oxidized purine DNA binding / ubiquitin-like protein conjugating enzyme binding / protein kinase A binding / laminin receptor activity / cellular response to actinomycin D / positive regulation of T cell receptor signaling pathway / TOR signaling / positive regulation of activated T cell proliferation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / protein-RNA complex assembly / spindle assembly / positive regulation of microtubule polymerization / positive regulation of cell cycle / laminin binding / rough endoplasmic reticulum / translation regulator activity / gastrulation / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA 3'-UTR binding / neural tube closure / small-subunit processome / Hsp90 protein binding / positive regulation of non-canonical NF-kappaB signal transduction / base-excision repair / mRNA 5'-UTR binding / transcription coactivator binding / response to virus / ruffle membrane / cellular response to hydrogen peroxide / cytoplasmic ribonucleoprotein granule / rRNA processing / kinase activity / cellular response to tumor necrosis factor / mitotic spindle / large ribosomal subunit / ribosome binding / cell body / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / microtubule binding / cytosolic large ribosomal subunit / DNA-binding transcription factor binding / cytoplasmic translation / mitochondrial inner membrane / negative regulation of translation / rRNA binding / postsynaptic density / protein stabilization / structural constituent of ribosome / positive regulation of apoptotic process / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / mRNA binding / apoptotic process / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / centrosome / protein kinase binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
: / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L30e / : / : / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type ...: / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L30e / : / : / 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 L41 / Ribosomal protein L41 / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / S27a-like superfamily / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L44e signature. / 40S Ribosomal protein S10 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / : / Ribosomal L40e family / Ribosomal protein S7e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L30e signature 1. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S17e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S17e signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S2, eukaryotic/archaeal / : / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein S27e signature. / Ribosomal protein S6, eukaryotic / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L18e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein S17e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS10 / 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 eL38 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S6 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL2 / 40S ribosomal protein S25 / Large ribosomal subunit protein eL33 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL20 / 40S ribosomal protein S12 / Small ribosomal subunit protein uS14 / Ribosomal protein L37 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL23 / 60S ribosomal protein L10 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL43 / 40S ribosomal protein S27 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS7 / 60S ribosomal protein L18 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS13 / Ribosomal protein L15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL14 / 60S ribosomal protein L27 / Ribosomal protein L19 / Large ribosomal subunit protein eL28 / 60S ribosomal protein L36a / 60S ribosomal protein L32 / Large ribosomal subunit protein eL24 / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4
Similarity search - Component
Biological speciesHeterocephalus glaber (naked mole-rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsGutierrez-Vargas, C. / De, S. / Maji, S. / Liu, Z. / Nieb, M. / Seluanov, A. / Gorbunova, V. / Frank, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139453 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P01 AG047200 United States
National Science Foundation (NSF, United States)DGE-1644869 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007061 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes-is rRNA fragmentation linked to translational fidelity?
Authors: Cristina Gutierrez-Vargas / Swastik De / Suvrajit Maji / Zheng Liu / Zhonghe Ke / Martina Nieß / Andrei Seluanov / Vera Gorbunova / Joachim Frank /
Abstract: Ribosomes are central to protein synthesis in all organisms. In mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco, ...Ribosomes are central to protein synthesis in all organisms. In mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco, display fragmented 28S ribosomal RNA (rRNA), coupled with high translational fidelity and long lifespan. The unusual ribosomal architecture in the NMR and tuco-tuco has been speculated to be linked to high translational fidelity. Here, we show, by single-particle cryo-electron microscopy, that despite the fragmentation of their rRNA, NMR and tuco-tuco ribosomes retain their core functional architecture. Compared to ribosomes of the guinea pig, a phylogenetically related rodent without 28S rRNA fragmentation, ribosomes of NMR and tuco-tuco exhibit poorly resolved density for certain expansion segments. In contrast, the structure of the guinea pig ribosome shows high similarity to the human ribosome. Enhanced translational fidelity in the NMR and tuco-tuco may stem from subtle, allosteric effects in dynamics, linked to rRNA fragmentation.
History
DepositionSep 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large ribosomal subunit protein uL2
B: 60S ribosomal protein L3
C: Large ribosomal subunit protein uL4
c: Large ribosomal subunit protein eL24
D: Large ribosomal subunit protein uL18
E: 60S ribosomal protein L6
F: 60S ribosomal protein L7
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L9
I: 60S ribosomal protein L10
J: Large ribosomal subunit protein uL5
L: 60S ribosomal protein L13
M: Large ribosomal subunit protein eL14
N: Ribosomal protein L15
O: 60S ribosomal protein L13a
P: 60S ribosomal protein L17
Q: 60S ribosomal protein L18
S: Large ribosomal subunit protein eL20
T: Large ribosomal subunit protein eL21
U: 60S ribosomal protein L22
V: Large ribosomal subunit protein uL14
W: Ribosomal protein L19
X: Large ribosomal subunit protein uL23
Y: 60S ribosomal protein L26
Z: 60S ribosomal protein L27
a: 60S ribosomal protein L27a
b: 60S ribosomal protein L29
d: Large ribosomal subunit protein eL31
e: 60S ribosomal protein L32
f: Large ribosomal subunit protein eL33
g: Large ribosomal subunit protein eL34
h: Large ribosomal subunit protein uL29
i: 60S ribosomal protein L36
j: Ribosomal protein L37
k: Large ribosomal subunit protein eL38
l: 60S ribosomal protein L39
m: Ubiquitin-ribosomal protein eL40 fusion protein
n: 60S ribosomal protein L41
o: 60S ribosomal protein L36a
p: Large ribosomal subunit protein eL43
r: Large ribosomal subunit protein eL28
s: 60S acidic ribosomal protein P0
t: 60S ribosomal protein L12
u: Large ribosomal subunit protein eL30
bb: 40S ribosomal protein S27
ee: 40S ribosomal protein S30
aa: 40S ribosomal protein S26
CC: 40S ribosomal protein S2
EE: 40S ribosomal protein S4, X isoform
GG: 40S ribosomal protein S6
HH: 40S ribosomal protein S7
II: 40S ribosomal protein S8
JJ: Small ribosomal subunit protein uS4
LL: Small ribosomal subunit protein uS17
NN: Small ribosomal subunit protein uS15
VV: 40S ribosomal protein S21
WW: Small ribosomal subunit protein uS8
XX: Small ribosomal subunit protein uS12
YY: 40S ribosomal protein S24
cc: 40S ribosomal protein S28
ff: Ubiquitin-ribosomal protein eS31 fusion protein
gg: Small ribosomal subunit protein RACK1
dd: Small ribosomal subunit protein uS14
AA: Small ribosomal subunit protein uS2
DD: Small ribosomal subunit protein uS3
FF: Small ribosomal subunit protein uS7
KK: Small ribosomal subunit protein eS10
MM: 40S ribosomal protein S12
PP: 40S ribosomal protein S15
QQ: Small ribosomal subunit protein uS9
SS: Small ribosomal subunit protein uS13
TT: Small ribosomal subunit protein eS19
UU: 40S ribosomal protein S20
ZZ: 40S ribosomal protein S25
EF: eEF2
Cc: P/E tRNA (77-MER)
A5: LSU alpha rRNA
A7: 5S ribosomal RNA
A8: 5.8S ribosomal RNA
B2: 18S ribosomal RNA
A6: LSU beta rRNA
BB: 40S ribosomal protein S3a
OO: 40S ribosomal protein S14
RR: Small ribosomal subunit protein eS17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,382,567118
Polymers3,381,41284
Non-polymers1,15534
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Large ribosomal subunit protein ... , 18 types, 18 molecules ACcDJMSTVXdfghkpru

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


Mass: 26998.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J3A4
#3: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 41251.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5AN81
#4: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 14131.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C020
#5: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34050.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6P0W2
#11: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11


Mass: 19399.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6TFX7
#13: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 16041.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5ALX1
#18: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JCV6
#19: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5ATV5
#21: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BK67
#23: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6PQW7
#28: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0N8ESF6
#30: 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
#31: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 12522.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5AQL2
#32: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14406.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B6W3
#35: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8107.752 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 eL43 / 60S ribosomal protein L37a


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: E3VX70
#41: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 14508.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BVZ2
#44: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 11127.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B8Y2

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60S ribosomal protein ... , 21 types, 21 molecules BEFGHILOPQUYZabeilnot

#2: Protein 60S ribosomal protein L3


Mass: 45603.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#6: Protein 60S ribosomal protein L6


Mass: 25390.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#7: Protein 60S ribosomal protein L7


Mass: 26658.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#8: Protein 60S ribosomal protein L7a


Mass: 24741.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#9: Protein 60S ribosomal protein L9


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#10: Protein 60S ribosomal protein L10


Mass: 24525.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6QHL6
#12: Protein 60S ribosomal protein L13


Mass: 23584.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#15: Protein 60S ribosomal protein L13a


Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#16: Protein 60S ribosomal protein L17


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#17: Protein 60S ribosomal protein L18


Mass: 21520.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B890
#20: Protein 60S ribosomal protein L22


Mass: 11481.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#24: Protein 60S ribosomal protein L26


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#25: Protein 60S ribosomal protein L27


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BN91
#26: Protein 60S ribosomal protein L27a


Mass: 16504.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#27: Protein 60S ribosomal protein L29


Mass: 12096.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#29: Protein 60S ribosomal protein L32


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BYD8
#33: Protein 60S ribosomal protein L36


Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#36: Protein/peptide 60S ribosomal protein L39


Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#38: 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
#39: Protein 60S ribosomal protein L36a / 60S ribosomal protein L36a-like


Mass: 12358.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BW65
#43: Protein 60S ribosomal protein L12


Mass: 16832.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)

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Ribosomal protein ... , 3 types, 3 molecules NWj

#14: Protein Ribosomal protein L15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BFP9
#22: Protein Ribosomal protein L19


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BRW3
#34: Protein Ribosomal protein L37


Mass: 10090.891 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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Ubiquitin-ribosomal protein ... , 2 types, 2 molecules mff

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


Mass: 6112.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C5A6
#61: Protein Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin carboxyl extension protein 80


Mass: 7884.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B8W4

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Protein , 2 types, 2 molecules sEF

#42: Protein 60S acidic ribosomal protein P0


Mass: 11822.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#75: Protein eEF2


Mass: 95232.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)

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40S ribosomal protein ... , 17 types, 17 molecules bbeeaaCCEEGGHHIIVVYYccMMPPUUZZBBOO

#45: Protein 40S ribosomal protein S27


Mass: 9210.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: E3VX74
#46: Protein/peptide 40S ribosomal protein S30


Mass: 5686.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#47: Protein 40S ribosomal protein S26


Mass: 11184.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#48: Protein 40S ribosomal protein S2


Mass: 24057.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#49: Protein 40S ribosomal protein S4, X isoform


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#50: Protein 40S ribosomal protein S6


Mass: 26399.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J125
#51: Protein 40S ribosomal protein S7


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5C7L2
#52: Protein 40S ribosomal protein S8


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#56: Protein 40S ribosomal protein S21


Mass: 9139.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#59: Protein 40S ribosomal protein S24


Mass: 14489.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0AAX6T3G5
#60: Protein 40S ribosomal protein S28


Mass: 6878.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#68: Protein 40S ribosomal protein S12


Mass: 13766.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JDT6
#69: Protein 40S ribosomal protein S15


Mass: 14002.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#73: Protein 40S ribosomal protein S20


Mass: 11324.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#74: Protein 40S ribosomal protein S25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J730
#82: Protein 40S ribosomal protein S3a


Mass: 25317.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#83: Protein 40S ribosomal protein S14


Mass: 14344.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)

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Small ribosomal subunit protein ... , 15 types, 15 molecules JJLLNNWWXXggddAADDFFKKQQSSTTRR

#53: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 21279.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5CBG2
#54: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 17328.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J0Q6
#55: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B0I4
#57: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5AY31
#58: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J0V6
#62: 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: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6J231
#63: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6JEN2
#64: 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: 24016.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6K1L6
#65: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 24956.264 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
#66: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 21327.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B7K7
#67: Protein Small ribosomal subunit protein eS10 / 40S ribosomal protein S10


Mass: 11529.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: A0A0P6IZJ7
#70: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BJD7
#71: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 16924.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5BAZ4
#72: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 15608.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5AZQ1
#84: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15250.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B1R5

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RNA chain , 6 types, 6 molecules CcA5A7A8B2A6

#76: RNA chain P/E tRNA (77-MER)


Mass: 24801.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heterocephalus glaber (naked mole-rat) / Production host: Heterocephalus glaber (naked mole-rat)
#77: RNA chain LSU alpha rRNA


Mass: 561151.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#78: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat) / References: GenBank: 2261261469
#79: RNA chain 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#80: RNA chain 18S ribosomal RNA


Mass: 592493.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)
#81: RNA chain LSU beta rRNA


Mass: 687220.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Heterocephalus glaber (naked mole-rat)

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Non-polymers , 3 types, 35 molecules

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


Mass: 24.305 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Mg
#86: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#87: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

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Sample preparation

ComponentName: Naked mole-rat ribosome / Type: RIBOSOME / Entity ID: #1-#84 / Source: NATURAL
Source (natural)Organism: Heterocephalus glaber (naked mole-rat)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMPotassium acetateCH3CO2K1
310 mMMagnesium acetateC4H6MgO41
42 mMDithiothreitolC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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 holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 6147

-
Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5 Å
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
14v6x

4v6x

4v6xrRNA chains1
2707y

707y

707yr-protein chains2
RefinementHighest resolution: 5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011244237
ELECTRON MICROSCOPYf_angle_d0.879357923
ELECTRON MICROSCOPYf_dihedral_angle_d25.833104234
ELECTRON MICROSCOPYf_chiral_restr0.04944333
ELECTRON MICROSCOPYf_plane_restr0.00823091

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