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- PDB-9y4g: Structure of tuco-tuco ribosome (rotated, tRNAs, and mRNA) -

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Basic information

Entry
Database: PDB / ID: 9y4g
TitleStructure of tuco-tuco ribosome (rotated, tRNAs, and mRNA)
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 42
  • 18S ribosomal RNA
  • 5.8S rRNA (157-MER)
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-2-like 1
  • LSU-alpha rRNA
  • LSU-beta rRNA (2108-MER)
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U*(MG))-3')
  • tRNA (77-MER)
  • tRNA (78-MER)
KeywordsRIBOSOME / Tuco tuco Ribosome
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesCtenomyidae (tuco-tucos)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGutierrez-Vargas, C. / De, S. / Maji, S. / Liu, Z. / Nieb, M. / Seluanov, A. / Gorbunova, V. / Frank, J.
Funding support United States, 3items
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
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
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Ag: Guanine nucleotide-binding protein subunit beta-2-like 1
AU: 40S ribosomal protein S20
AK: 40S ribosomal protein S10
AM: 40S ribosomal protein S12
AS: 40S ribosomal protein S18
Ad: 40S ribosomal protein S29
AR: 40S ribosomal protein S17
AP: 40S ribosomal protein S15
AT: 40S ribosomal protein S19
AZ: 40S ribosomal protein S25
Ac: 40S ribosomal protein S28
AD: 40S ribosomal protein S3
Af: 40S ribosomal protein S27a
AF: 40S ribosomal protein S5
AQ: 40S ribosomal protein S16
B2: 18S ribosomal RNA
AO: 40S ribosomal protein S14
AX: 40S ribosomal protein S23
AN: 40S ribosomal protein S13
AL: 40S ribosomal protein S11
AB: 40S ribosomal protein S3a
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: 40S ribosomal protein S30
AJ: 40S ribosomal protein S9
AE: 40S ribosomal protein S4, X isoform
AC: 40S ribosomal protein S2
AG: 40S ribosomal protein S6
AH: 40S ribosomal protein S7
AW: 40S ribosomal protein S15a
AI: 40S ribosomal protein S8
CR: 60S ribosomal protein L19
CW: 60S ribosomal protein L24
Cz: 60S ribosomal protein L10a
CO: 60S ribosomal protein L13a
CL: 60S ribosomal protein L13
CV: 60S ribosomal protein L23
CM: 60S ribosomal protein L14
Ca: 60S ribosomal protein L27a
CN: 60S ribosomal protein L15
CI: 60S ribosomal protein L10-like
CD: 60S ribosomal protein L5
CQ: 60S ribosomal protein L18
CA: 60S ribosomal protein L8
CS: 60S ribosomal protein L18a
CT: 60S ribosomal protein L21
CP: 60S ribosomal protein L17
CU: 60S ribosomal protein L22
CX: 60S ribosomal protein L23a
CY: 60S ribosomal protein L26
CZ: 60S ribosomal protein L27
Cr: 60S ribosomal protein L28
Ch: 60S ribosomal protein L35
Cb: 60S ribosomal protein L29
CB: 60S ribosomal protein L3
CF: 60S ribosomal protein L7
Cd: 60S ribosomal protein L31
Ce: 60S ribosomal protein L32
Cf: 60S ribosomal protein L35a
Cg: 60S ribosomal protein L34
Ci: 60S ribosomal protein L36
Cj: 60S ribosomal protein L37
Ck: 60S ribosomal protein L38
Cl: 60S ribosomal protein L39
CC: 60S ribosomal protein L4
Cm: 60S ribosomal protein L40
Cn: 60S ribosomal protein L41
Cp: 60S ribosomal protein L37a
Co: 60S ribosomal protein L36a
CJ: 60S ribosomal protein L11
CH: 60S ribosomal protein L9
CE: 60S ribosomal protein L6
CG: 60S ribosomal protein L7a
A5: LSU-alpha rRNA
A7: 5S ribosomal RNA
A8: 5.8S rRNA (157-MER)
Cc: tRNA (78-MER)
Bb: tRNA (77-MER)
Dd: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U*(MG))-3')
A6: LSU-beta rRNA (2108-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,317,40486
Polymers3,317,33283
Non-polymers733
Water27015
1


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

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Components

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Protein , 1 types, 1 molecules Ag

#1: Protein Guanine nucleotide-binding protein subunit beta-2-like 1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)

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40S ribosomal protein ... , 32 types, 32 molecules AUAKAMASAdARAPATAZAcADAfAFAQAOAXANALABAAAVAYAaAbAeAJAEACAGAHAWAI

#2: Protein 40S ribosomal protein S20


Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#3: Protein 40S ribosomal protein S10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#4: Protein 40S ribosomal protein S12


Mass: 13776.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#5: Protein 40S ribosomal protein S18


Mass: 16170.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#6: Protein 40S ribosomal protein S29


Mass: 6364.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#7: Protein 40S ribosomal protein S17


Mass: 14578.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#8: Protein 40S ribosomal protein S15


Mass: 15178.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#9: Protein 40S ribosomal protein S19


Mass: 15668.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenomyidae (tuco-tucos) / Production host: Ctenomyidae (tuco-tucos)
#10: Protein 40S ribosomal protein S25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#11: Protein 40S ribosomal protein S28


Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#12: Protein 40S ribosomal protein S3


Mass: 25172.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#13: Protein 40S ribosomal protein S27a


Mass: 8358.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#14: Protein 40S ribosomal protein S5


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#15: Protein 40S ribosomal protein S16


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#17: Protein 40S ribosomal protein S14


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#18: Protein 40S ribosomal protein S23


Mass: 15757.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#19: Protein 40S ribosomal protein S13


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#20: Protein 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#21: Protein 40S ribosomal protein S3a


Mass: 25017.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#22: Protein 40S ribosomal protein SA


Mass: 23360.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#23: Protein 40S ribosomal protein S21


Mass: 8977.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#24: Protein 40S ribosomal protein S24


Mass: 14604.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#25: Protein 40S ribosomal protein S26


Mass: 12110.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#26: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#27: Protein 40S ribosomal protein S30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#28: Protein 40S ribosomal protein S9


Mass: 21266.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#29: Protein 40S ribosomal protein S4, X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#30: Protein 40S ribosomal protein S2


Mass: 24961.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#31: Protein 40S ribosomal protein S6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#32: Protein 40S ribosomal protein S7


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#33: Protein 40S ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#34: Protein 40S ribosomal protein S8


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)

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RNA chain , 8 types, 8 molecules B2A5A7A8CcBbDdA6

#16: RNA chain 18S ribosomal RNA


Mass: 579439.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#77: RNA chain LSU-alpha rRNA


Mass: 575951.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#78: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#79: RNA chain 5.8S rRNA (157-MER)


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#80: RNA chain tRNA (78-MER)


Mass: 24801.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#81: RNA chain tRNA (77-MER)


Mass: 24743.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#82: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U*(MG))-3')


Mass: 3935.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#83: RNA chain LSU-beta rRNA (2108-MER)


Mass: 682418.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)

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60S ribosomal protein ... , 42 types, 42 molecules CRCWCzCOCLCVCMCaCNCICDCQCACSCTCPCUCXCYCZCrChCbCBCFCdCeCfCgCi...

#35: Protein 60S ribosomal protein L19


Mass: 22659.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#36: Protein 60S ribosomal protein L24


Mass: 14476.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#37: Protein 60S ribosomal protein L10a


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#38: Protein 60S ribosomal protein L13a


Mass: 23502.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#39: Protein 60S ribosomal protein L13


Mass: 24190.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#40: Protein 60S ribosomal protein L23


Mass: 14116.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#41: Protein 60S ribosomal protein L14


Mass: 16254.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#42: Protein 60S ribosomal protein L27a


Mass: 16473.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#43: Protein 60S ribosomal protein L15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#44: Protein 60S ribosomal protein L10-like


Mass: 24439.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#45: Protein 60S ribosomal protein L5


Mass: 33535.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#46: Protein 60S ribosomal protein L18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#47: Protein 60S ribosomal protein L8


Mass: 27843.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#48: Protein 60S ribosomal protein L18a


Mass: 20677.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#49: Protein 60S ribosomal protein L21


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#50: Protein 60S ribosomal protein L17


Mass: 17628.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#51: Protein 60S ribosomal protein L22


Mass: 13098.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#52: Protein 60S ribosomal protein L23a


Mass: 14114.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#53: Protein 60S ribosomal protein L26


Mass: 15760.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#54: Protein 60S ribosomal protein L27


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#55: Protein 60S ribosomal protein L28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#56: Protein 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#57: Protein 60S ribosomal protein L29


Mass: 9077.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#58: Protein 60S ribosomal protein L3


Mass: 45564.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#59: Protein 60S ribosomal protein L7


Mass: 27163.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#60: Protein 60S ribosomal protein L31


Mass: 13250.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#61: Protein 60S ribosomal protein L32


Mass: 15655.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#62: Protein 60S ribosomal protein L35a


Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#63: Protein 60S ribosomal protein L34


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#64: Protein 60S ribosomal protein L36


Mass: 12046.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#65: Protein 60S ribosomal protein L37


Mass: 10489.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#66: Protein 60S ribosomal protein L38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#67: Protein/peptide 60S ribosomal protein L39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#68: Protein 60S ribosomal protein L4


Mass: 41683.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#69: Protein 60S ribosomal protein L40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#70: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#71: Protein 60S ribosomal protein L37a


Mass: 10097.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#72: Protein 60S ribosomal protein L36a


Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#73: Protein 60S ribosomal protein L11


Mass: 19213.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#74: Protein 60S ribosomal protein L9


Mass: 21770.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#75: Protein 60S ribosomal protein L6


Mass: 30020.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)
#76: Protein 60S ribosomal protein L7a


Mass: 28039.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ctenomyidae (tuco-tucos)

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Non-polymers , 2 types, 18 molecules

#84: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#85: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Tuco tuco Ribosome / Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ctenomyidae (tuco-tucos)
Buffer solutionpH: 7.5
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
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 17093

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2EPUimage acquisition
12RELION3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1296629
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232230 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4v6x

4v6x


Accession code: 4v6x / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.3 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005235886
ELECTRON MICROSCOPYf_angle_d1.34346866
ELECTRON MICROSCOPYf_dihedral_angle_d24.344102623
ELECTRON MICROSCOPYf_chiral_restr0.05943199
ELECTRON MICROSCOPYf_plane_restr0.01121801

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