ISDA: 9Y49

Deposition Date 2025-09-02

Release Date 2026-02-18

Last Version Date 2026-02-18

Entry Detail

PDB ID:

9Y49

Keywords:

RIBOSOME

Title:

Structure of tuco-tuco ribosome with P/E tRNA and eEF2 (rotated)

Biological Source:

Source Organism(s):

Ctenomyidae (Taxon ID: 30645)

Expression System(s):

Ctenomyidae

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:LSU-alpha rRNA (1722-MER)
Chain IDs:AC (auth: A5)
Chain Length:1722
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polyribonucleotide
Molecule:LSU-beta rRNA (2069-MER)
Chain IDs:DC (auth: A6)
Chain Length:2069
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polyribonucleotide
Molecule:5S rRNA (121-MER)
Chain IDs:BC (auth: A7)
Chain Length:121
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA (157-MER)
Chain IDs:CC (auth: A8)
Chain Length:157
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Chain IDs:H (auth: AA)
Chain Length:208
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Chain IDs:G (auth: AB)
Chain Length:212
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:P (auth: AC)
Chain Length:220
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Chain IDs:HA (auth: AD)
Chain Length:227
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Chain IDs:O (auth: AE)
Chain Length:262
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Chain IDs:JA (auth: AF)
Chain Length:71
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:Q (auth: AG)
Chain Length:237
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:R (auth: AH)
Chain Length:189
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Chain IDs:T (auth: AI)
Chain Length:206
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Chain IDs:N (auth: AJ)
Chain Length:178
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Chain IDs:Y (auth: AK)
Chain Length:98
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Chain IDs:F (auth: AL)
Chain Length:157
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Chain IDs:Z (auth: AM)
Chain Length:122
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:E (auth: AN)
Chain Length:149
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Chain IDs:C (auth: AO)
Chain Length:136
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Chain IDs:DA (auth: AP)
Chain Length:124
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Chain IDs:KA (auth: AQ)
Chain Length:141
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Chain IDs:CA (auth: AR)
Chain Length:126
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Chain IDs:AA (auth: AS)
Chain Length:137
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Chain IDs:EA (auth: AT)
Chain Length:141
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Chain IDs:X (auth: AU)
Chain Length:104
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Chain IDs:I (auth: AV)
Chain Length:82
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Chain IDs:S (auth: AW)
Chain Length:129
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Chain IDs:D (auth: AX)
Chain Length:139
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:J (auth: AY)
Chain Length:126
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Chain IDs:FA (auth: AZ)
Chain Length:75
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Chain IDs:K (auth: Aa)
Chain Length:208
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:L (auth: Ab)
Chain Length:212
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Chain IDs:GA (auth: Ac)
Chain Length:220
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Chain IDs:BA (auth: Ad)
Chain Length:227
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Chain IDs:M (auth: Ae)
Chain Length:262
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27a
Chain IDs:IA (auth: Af)
Chain Length:71
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-2-like 1
Chain IDs:W (auth: Ag)
Chain Length:237
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polyribonucleotide
Molecule:18S rRNA (1786-MER)
Chain IDs:U (auth: B2)
Chain Length:1786
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Chain IDs:VA (auth: CA)
Chain Length:147
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Chain IDs:GB (auth: CB)
Chain Length:73
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Chain IDs:RB (auth: CC)
Chain Length:365
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:TA (auth: CD)
Chain Length:113
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:YB (auth: CE)
Chain Length:254
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Chain IDs:HB (auth: CF)
Chain Length:109
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Chain IDs:ZB (auth: CG)
Chain Length:246
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Chain IDs:XB (auth: CH)
Chain Length:123
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10-like
Chain IDs:SA (auth: CI)
Chain Length:207
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Chain IDs:WB (auth: CJ)
Chain Length:89
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:NA (auth: CL)
Chain Length:208
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Chain IDs:PA (auth: CM)
Chain Length:50
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Chain IDs:RA (auth: CN)
Chain Length:24
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Chain IDs:MA (auth: CO)
Chain Length:199
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Chain IDs:YA (auth: CP)
Chain Length:152
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Chain IDs:UA (auth: CQ)
Chain Length:188
Number of Molecules:1
Biological Source:Ctenomyidae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19
Gene (Uniprot):RPL19
Chain IDs:EC (auth: CR)
Chain Length:189
Number of Molecules:1
Biological Source:Ctenomyidae

UniProt ID:Q3T0W9 Pfam ID:PF01280, PF25476

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Chain IDs:WA (auth: CS)
Chain Length:175
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Chain IDs:XA (auth: CT)
Chain Length:847
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Chain IDs:ZA (auth: CU)
Chain Length:110
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Chain IDs:OA (auth: CV)
Chain Length:132
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Chain IDs:V (auth: CW)
Chain Length:124
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Chain IDs:AB (auth: CX)
Chain Length:121
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Chain IDs:BB (auth: CY)
Chain Length:133
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:CB (auth: CZ)
Chain Length:135
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Chain IDs:QA (auth: Ca)
Chain Length:147
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:FB (auth: Cb)
Chain Length:73
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Chain IDs:IB (auth: Cc)
Chain Length:365
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Chain IDs:JB (auth: Cd)
Chain Length:113
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Chain IDs:KB (auth: Ce)
Chain Length:254
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Chain IDs:LB (auth: Cf)
Chain Length:109
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Chain IDs:MB (auth: Cg)
Chain Length:246
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Chain IDs:EB (auth: Ch)
Chain Length:123
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Chain IDs:NB (auth: Ci)
Chain Length:207
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Chain IDs:OB (auth: Cj)
Chain Length:89
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Chain IDs:PB (auth: Ck)
Chain Length:68
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Chain IDs:QB (auth: Cl)
Chain Length:208
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L40
Chain IDs:SB (auth: Cm)
Chain Length:50
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Chain IDs:TB (auth: Cn)
Chain Length:24
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36a
Chain IDs:VB (auth: Co)
Chain Length:199
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Chain IDs:UB (auth: Cp)
Chain Length:152
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Chain IDs:DB (auth: Cr)
Chain Length:189
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:Elongation factor 2
Chain IDs:B (auth: Ct)
Chain Length:847
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10a
Chain IDs:LA (auth: Cz)
Chain Length:135
Number of Molecules:1
Biological Source:Ctenomyidae

Polymer Type:polyribonucleotide
Molecule:tRNA (77-MER)
Chain IDs:A (auth: tR)
Chain Length:77
Number of Molecules:1
Biological Source:Ctenomyidae

Ligand Molecules

Primary Citation

Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes-is rRNA fragmentation linked to translational fidelity?

Gutierrez-Vargas, C, De, S, Maji, S, Liu, Z, Ke, Z, Niess, M, Seluanov, A, Gorbunova, V, Frank, J.Show

Nucleic Acids Res. 54 ? ? (2026)

PMID: 41603730 DOI: 10.1093/nar/gkag006

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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