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- PDB-9y4h: Structure of guinea pig ribosome with P/E-tRNA and mRNA -

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Basic information

Entry
Database: PDB / ID: 9y4h
TitleStructure of guinea pig ribosome with P/E-tRNA and mRNA
Components
  • (40S ribosomal protein ...) x 17
  • (60S ribosomal protein ...) x 24
  • (Large ribosomal subunit protein ...) x 12
  • (Ribosomal protein ...) x 4
  • (Small ribosomal subunit protein ...) x 13
  • 18S rRNA (1803-MER)
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • FAU ubiquitin like and ribosomal protein S30 fusion
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • mRNA
  • tRNA
KeywordsRIBOSOME / Guinea pig ribosome
Function / homology
Function and homology information


translation at postsynapse / translation at presynapse / eukaryotic 80S initiation complex / axial mesoderm development / regulation of G1 to G0 transition / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport ...translation at postsynapse / translation at presynapse / eukaryotic 80S initiation complex / axial mesoderm development / regulation of G1 to G0 transition / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition / cysteine-type endopeptidase activator activity involved in apoptotic process / neural crest cell differentiation / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / ion channel inhibitor activity / pigmentation / positive regulation of mitochondrial depolarization / cellular response to actinomycin D / BH3 domain binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein serine/threonine kinase inhibitor activity / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / regulation of translational fidelity / phagocytic cup / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of cell cycle / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / signaling adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / stress granule assembly / rescue of stalled cytosolic ribosome / SH2 domain binding / ossification / cyclin binding / protein kinase C binding / cellular response to leukemia inhibitory factor / skeletal system development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / negative regulation of smoothened signaling pathway / mRNA 3'-UTR binding / neural tube closure / cellular response to glucose stimulus / small-subunit processome / positive regulation of protein-containing complex assembly / sensory perception of sound / negative regulation of cell growth / receptor tyrosine kinase binding / maintenance of translational fidelity / mRNA 5'-UTR binding / cellular response to growth factor stimulus / transcription coactivator binding / response to virus / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of translation / large ribosomal subunit / antibacterial humoral response / presynapse / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / midbody / protein phosphatase binding / cytosolic large ribosomal subunit / killing of cells of another organism / defense response to Gram-negative bacterium / cytoplasmic translation / cell differentiation / regulation of cell cycle / postsynapse / rRNA binding / postsynaptic density / protein stabilization / positive regulation of cell migration / defense response to Gram-positive bacterium / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / negative regulation of gene expression / neuronal cell body / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding
Similarity search - Function
: / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. ...: / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / : / : / Ribosomal L40e family / Ribosomal protein S7e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L30/YlxQ / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S27e signature. / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S8e / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein L21e / Ribosomal protein S3Ae / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal S3Ae family / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal S3Ae family / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L24e-related
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL43 / 40S ribosomal protein S24 / 40S ribosomal protein S15 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL43 / 40S ribosomal protein S24 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS14 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL24 / Ribosomal protein L37 / Ribosomal protein L15 / Large ribosomal subunit protein eL31 / 40S ribosomal protein S8 / 40S ribosomal protein S21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL38 / Ribosomal protein L36a / 40S ribosomal protein S7 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S25 / FAU ubiquitin like and ribosomal protein S30 fusion / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S27 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS19 / Ribosomal protein L32 / Small ribosomal subunit protein uS7 / 60S ribosomal protein L36
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 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 3, 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
AO: 40S ribosomal protein S14
AX: Small ribosomal subunit protein uS12
AN: 40S ribosomal protein S13
AL: Small ribosomal subunit protein uS17
AB: Small ribosomal subunit protein eS1
AA: 40S ribosomal protein SA
AV: 40S ribosomal protein S21
AY: 40S ribosomal protein S24
Aa: 40S ribosomal protein S26
Ab: 40S ribosomal protein S27
Ae: FAU ubiquitin like and ribosomal protein S30 fusion
AJ: Small ribosomal subunit protein uS4
AE: 40S ribosomal protein S4, X isoform
AC: 40S ribosomal protein S2
AG: 40S ribosomal protein S6
AH: 40S ribosomal protein S7
AW: Small ribosomal subunit protein uS8
AI: 40S ribosomal protein S8
B2: 18S rRNA (1803-MER)
CW: Large ribosomal subunit protein eL24
Ag: Small ribosomal subunit protein RACK1
AU: Small ribosomal subunit protein uS10
AK: 40S ribosomal protein S10
AS: Small ribosomal subunit protein uS13
Ad: Small ribosomal subunit protein uS14
AR: Small ribosomal subunit protein eS17
AP: 40S ribosomal protein S15
AT: Small ribosomal subunit protein eS19
AZ: 40S ribosomal protein S25
Ac: 40S ribosomal protein S28
AD: 40S ribosomal protein S3
AF: Small ribosomal subunit protein uS7
AQ: Small ribosomal subunit protein uS9
CO: 60S ribosomal protein L13a
CL: 60S ribosomal protein L13
CV: Large ribosomal subunit protein uL14
CM: 60S ribosomal protein L14
Ca: 60S ribosomal protein L27a
CN: Ribosomal protein L15
CI: 60S ribosomal protein L10-like
CD: 60S ribosomal protein L5
CQ: 60S ribosomal protein L18
CA: Large ribosomal subunit protein uL2
CS: 60S ribosomal protein L18a
CT: Large ribosomal subunit protein eL21
CP: 60S ribosomal protein L17
CU: 60S ribosomal protein L22
CX: 60S ribosomal protein L23a
CY: Large ribosomal subunit protein uL24
CZ: 60S ribosomal protein L27
Cr: Large ribosomal subunit protein eL28
Ch: 60S ribosomal protein L35
Cb: 60S ribosomal protein L29
CB: 60S ribosomal protein L3
CF: 60S ribosomal protein L7
Cc: Large ribosomal subunit protein eL30
Cd: Large ribosomal subunit protein eL31
Ce: Ribosomal protein L32
Cf: 60S ribosomal protein L35a
Cg: Large ribosomal subunit protein eL34
Ci: 60S ribosomal protein L36
Cj: Ribosomal protein L37
Ck: Large ribosomal subunit protein eL38
Cl: 60S ribosomal protein L39
CC: 60S ribosomal protein L4
Cm: Ubiquitin-ribosomal protein eL40 fusion protein
Cn: 60S ribosomal protein L41
Cp: Large ribosomal subunit protein eL43
Co: Ribosomal protein L36a
CJ: Large ribosomal subunit protein uL5
CH: 60S ribosomal protein L9
CE: 60S ribosomal protein L6
CG: 60S ribosomal protein L7a
A5: 28S ribosomal RNA
A7: 5S ribosomal RNA
A8: 5.8S ribosomal RNA
Cw: tRNA
Dd: mRNA


Theoretical massNumber of molelcules
Total (without water)3,379,76278
Polymers3,379,76278
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#3: Protein 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#6: Protein 40S ribosomal protein SA


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#7: Protein 40S ribosomal protein S21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0UXF6
#8: Protein 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XEI0
#9: Protein 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#10: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VV27
#13: Protein 40S ribosomal protein S4, X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#14: Protein 40S ribosomal protein S2


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#15: Protein 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#16: Protein 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VFF0
#18: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0UUK1
#23: Protein 40S ribosomal protein S10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#27: Protein 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XFR1
#29: Protein 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VNE6
#30: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#31: Protein 40S ribosomal protein S3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)

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Small ribosomal subunit protein ... , 13 types, 13 molecules AXALABAJAWAgAUASAdARATAFAQ

#2: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XV32
#4: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VSN8
#5: Protein Small ribosomal subunit protein eS1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VTN3
#12: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0W169
#17: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286X9S8
#21: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VCZ6
#22: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VJS8
#24: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0W478
#25: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XIF3
#26: Protein Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#28: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0W551
#32: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: H0WBB4
#33: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XLU0

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Protein , 2 types, 2 molecules AeCm

#11: Protein FAU ubiquitin like and ribosomal protein S30 fusion


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VRN6
#66: Protein Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XB24

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RNA chain , 6 types, 6 molecules B2A5A7A8CwDd

#19: RNA chain 18S rRNA (1803-MER)


Mass: 581520.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#74: RNA chain 28S ribosomal RNA


Mass: 1298775.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#75: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: GenBank: 38606971
#76: RNA chain 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#77: RNA chain tRNA


Mass: 24801.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#78: RNA chain mRNA


Mass: 2098.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)

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Large ribosomal subunit protein ... , 12 types, 12 molecules CWCVCACTCYCrCcCdCgCkCpCJ

#20: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XVX7
#36: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VFW4
#43: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VXR3
#45: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VVZ0
#49: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XLT0
#51: Protein Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#56: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XUT8
#57: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286Y4P0
#60: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XLF0
#63: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VDL2
#68: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XCQ6
#70: 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) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XPZ2

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60S ribosomal protein ... , 24 types, 24 molecules COCLCMCaCICDCQCSCPCUCXCZChCbCBCFCfCiClCCCnCHCECG

#34: Protein 60S ribosomal protein L13a


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#35: Protein 60S ribosomal protein L13


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#37: Protein 60S ribosomal protein L14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#38: Protein 60S ribosomal protein L27a


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#40: Protein 60S ribosomal protein L10-like


Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#41: Protein 60S ribosomal protein L5


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#42: Protein 60S ribosomal protein L18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#44: Protein 60S ribosomal protein L18a


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#46: Protein 60S ribosomal protein L17


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#47: Protein 60S ribosomal protein L22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#48: Protein 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#50: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#52: Protein 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#53: Protein 60S ribosomal protein L29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#54: Protein 60S ribosomal protein L3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#55: Protein 60S ribosomal protein L7


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#59: Protein 60S ribosomal protein L35a


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#61: Protein 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0WCA3
#64: Protein 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#65: Protein 60S ribosomal protein L4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#67: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XJA3
#71: Protein 60S ribosomal protein L9


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#72: Protein 60S ribosomal protein L6


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)
#73: Protein 60S ribosomal protein L7a


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig)

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Ribosomal protein ... , 4 types, 4 molecules CNCeCjCo

#39: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286Y424
#58: Protein Ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0W7S0
#62: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: A0A286XX70
#69: Protein Ribosomal protein L36a


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: H0VDY1

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Non-polymers , 1 types, 7 molecules

#79: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Guinea Pig Ribosome / Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cavia porcellus (domestic guinea pig)
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: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
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
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3904

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2Leginonimage acquisition
4CTFFINDCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 194700
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42298 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 4V6X

4v6x


Accession code: 4V6X / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 245.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0041231310
ELECTRON MICROSCOPYf_angle_d0.8793340685
ELECTRON MICROSCOPYf_chiral_restr0.047642506
ELECTRON MICROSCOPYf_plane_restr0.008321106
ELECTRON MICROSCOPYf_dihedral_angle_d24.5705102061

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