9Y4H image
Deposition Date 2025-09-03
Release Date 2026-02-18
Last Version Date 2026-02-18
Entry Detail
PDB ID:
9Y4H
Keywords:
RIBOSOME
Title:
Structure of guinea pig ribosome with P/E-tRNA and mRNA
Biological Source:
Source Organism(s):
Cavia porcellus (Taxon ID: 10141)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9Y4H validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:VB (auth: A5)
Chain Length:4010
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:WB (auth: A7)
Chain Length:121
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:XB (auth: A8)
Chain Length:157
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Chain IDs:F (auth: AA)
Chain Length:295
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS1
Chain IDs:E (auth: AB)
Chain Length:84
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:N (auth: AC)
Chain Length:293
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Chain IDs:EA (auth: AD)
Chain Length:56
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Chain IDs:M (auth: AE)
Chain Length:263
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Chain IDs:FA (auth: AF)
Chain Length:204
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:O (auth: AG)
Chain Length:249
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:P (auth: AH)
Chain Length:194
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Chain IDs:R (auth: AI)
Chain Length:208
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Chain IDs:L (auth: AJ)
Chain Length:194
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Chain IDs:W (auth: AK)
Chain Length:165
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Chain IDs:D (auth: AL)
Chain Length:158
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:C (auth: AN)
Chain Length:151
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Chain IDs:A (auth: AO)
Chain Length:151
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Chain IDs:AA (auth: AP)
Chain Length:145
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Chain IDs:GA (auth: AQ)
Chain Length:146
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17
Chain IDs:Z (auth: AR)
Chain Length:135
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Chain IDs:X (auth: AS)
Chain Length:152
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19
Chain IDs:BA (auth: AT)
Chain Length:145
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Chain IDs:V (auth: AU)
Chain Length:119
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Chain IDs:G (auth: AV)
Chain Length:83
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Chain IDs:Q (auth: AW)
Chain Length:130
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Chain IDs:B (auth: AX)
Chain Length:143
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:H (auth: AY)
Chain Length:133
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Chain IDs:CA (auth: AZ)
Chain Length:125
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Chain IDs:I (auth: Aa)
Chain Length:295
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:J (auth: Ab)
Chain Length:84
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Chain IDs:DA (auth: Ac)
Chain Length:293
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Chain IDs:Y (auth: Ad)
Chain Length:56
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:FAU ubiquitin like and ribosomal protein S30 fusion
Chain IDs:K (auth: Ae)
Chain Length:263
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein RACK1
Chain IDs:U (auth: Ag)
Chain Length:249
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polyribonucleotide
Molecule:18S rRNA (1803-MER)
Chain IDs:S (auth: B2)
Chain Length:1803
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Chain IDs:QA (auth: CA)
Chain Length:257
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Chain IDs:BB (auth: CB)
Chain Length:403
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Chain IDs:MB (auth: CC)
Chain Length:115
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:OA (auth: CD)
Chain Length:125
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:TB (auth: CE)
Chain Length:135
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Chain IDs:CB (auth: CF)
Chain Length:110
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Chain IDs:UB (auth: CG)
Chain Length:266
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Chain IDs:SB (auth: CH)
Chain Length:123
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10-like
Chain IDs:NA (auth: CI)
Chain Length:214
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Chain IDs:RB (auth: CJ)
Chain Length:97
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:IA (auth: CL)
Chain Length:211
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Chain IDs:KA (auth: CM)
Chain Length:52
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Chain IDs:MA (auth: CN)
Chain Length:25
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Chain IDs:HA (auth: CO)
Chain Length:106
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Chain IDs:TA (auth: CP)
Chain Length:184
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Chain IDs:PA (auth: CQ)
Chain Length:188
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Chain IDs:RA (auth: CS)
Chain Length:176
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21
Chain IDs:SA (auth: CT)
Chain Length:160
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Chain IDs:UA (auth: CU)
Chain Length:128
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Chain IDs:JA (auth: CV)
Chain Length:140
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24
Chain IDs:T (auth: CW)
Chain Length:157
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Chain IDs:VA (auth: CX)
Chain Length:156
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Chain IDs:WA (auth: CY)
Chain Length:145
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:XA (auth: CZ)
Chain Length:136
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Chain IDs:LA (auth: Ca)
Chain Length:257
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:AB (auth: Cb)
Chain Length:403
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30
Chain IDs:DB (auth: Cc)
Chain Length:115
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31
Chain IDs:EB (auth: Cd)
Chain Length:125
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L32
Chain IDs:FB (auth: Ce)
Chain Length:135
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Chain IDs:GB (auth: Cf)
Chain Length:110
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34
Chain IDs:HB (auth: Cg)
Chain Length:266
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Chain IDs:ZA (auth: Ch)
Chain Length:123
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Chain IDs:IB (auth: Ci)
Chain Length:214
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Chain IDs:JB (auth: Cj)
Chain Length:97
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL38
Chain IDs:KB (auth: Ck)
Chain Length:70
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Chain IDs:LB (auth: Cl)
Chain Length:211
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein eL40 fusion protein
Chain IDs:NB (auth: Cm)
Chain Length:52
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Chain IDs:OB (auth: Cn)
Chain Length:25
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L36a
Chain IDs:QB (auth: Co)
Chain Length:106
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43
Chain IDs:PB (auth: Cp)
Chain Length:184
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL28
Chain IDs:YA (auth: Cr)
Chain Length:137
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:YB (auth: Cw)
Chain Length:157
Number of Molecules:1
Biological Source:Cavia porcellus
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:ZB (auth: Dd)
Chain Length:7
Number of Molecules:1
Biological Source:Cavia porcellus
Primary Citation
Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes-is rRNA fragmentation linked to translational fidelity?
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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Disease

Primary Citation of related structures
9Y4H
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