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- PDB-9x4i: Structure of the young Killifish Ribosome -

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Basic information

Entry
Database: PDB / ID: 9x4i
TitleStructure of the young Killifish Ribosome
Components
  • (40S ribosomal protein ...) x 10
  • (60S ribosomal protein ...) x 8
  • (Large ribosomal subunit protein ...) x 25
  • (Ribosomal protein ...) x 8
  • (Small ribosomal subunit protein ...) x 19
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DNA-(apurinic or apyrimidinic site) lyase
  • FAU ubiquitin like and ribosomal protein S30 fusion a
  • Ubiquitin-ribosomal protein eL40 fusion protein
KeywordsRIBOSOME / ribosome dynamics / ribosome associated quality control / Nothobranchius furzeri / aging / skeletal muscle
Function / homology
Function and homology information


embryonic brain development / protein-RNA complex assembly / laminin receptor activity / 90S preribosome / translation regulator activity / rough endoplasmic reticulum / laminin binding / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity ...embryonic brain development / protein-RNA complex assembly / laminin receptor activity / 90S preribosome / translation regulator activity / rough endoplasmic reticulum / laminin binding / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / ribosome biogenesis / spindle / rRNA processing / cytosolic ribosome / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / mitochondrial inner membrane / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / endoplasmic reticulum / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L13e / Ribosomal L38e protein family / Ribosomal protein S21e / Ribosomal protein L38e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / : / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein S7e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S17e, conserved site / Ribosomal protein L40e superfamily / Ribosomal protein S17e signature. / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L7A/L8 / 60S ribosomal protein L35
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL31 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL31 / 60S ribosomal protein L36 / Ribosomal protein L37 / 40S ribosomal protein S21 / Small ribosomal subunit protein uS9 / 40S ribosomal protein S25 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL13 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL2 / 40S ribosomal protein S15 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S4 / Small ribosomal subunit protein uS2 / Ribosomal protein S10 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL29 / 60S ribosomal protein L36a / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Ribosomal protein L26 / Ribosomal protein L19 / 60S ribosomal protein L7a / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS1 / Ribosomal protein L15 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L27 / Ribosomal protein L18 / Large ribosomal subunit protein uL3 / DNA-(apurinic or apyrimidinic site) lyase / 60S ribosomal protein L18a / Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL13 / 40S ribosomal protein S8 / 60S ribosomal protein L32 / Large ribosomal subunit protein eL21 / Ribosomal protein L10 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L29 / Small ribosomal subunit protein uS8 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4 / 40S ribosomal protein S24 / Large ribosomal subunit protein eL28 / Ribosomal protein L4 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S26 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS32
Similarity search - Component
Biological speciesNothobranchius furzeri (turquoise killifish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsKim, J. / Song, J.J. / Kim, Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00333346 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00266300 Korea, Republic Of
CitationJournal: To Be Published
Title: Ribosome remodels in age-dependent manner
Authors: Kim, J. / Hyeon, D.Y. / Lee, S. / Ryu, B.H. / Gwak, N. / Choi, Y. / Vu, H.M. / Huh, S. / Kim, S. / Myung, K. / Dieterich, C. / Valenzano, D.R. / Kim, M.S. / Hwang, D. / Song, J.J. / Kim, Y.
History
DepositionOct 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
11: Large ribosomal subunit protein eL39
21: Ubiquitin-ribosomal protein eL40 fusion protein
32: 40S ribosomal protein S27
41: Large ribosomal subunit protein eL28
42: Small ribosomal subunit protein eS1
51: Small ribosomal subunit protein eS32
61: Ribosomal protein L10
71: Large ribosomal subunit protein uL5
72: Small ribosomal subunit protein uS11
81: Large ribosomal subunit protein uL13
82: 40S ribosomal protein S26
91: Large ribosomal subunit protein eL30
A1: 28S rRNA
A2: 40S ribosomal protein S15
B1: Large ribosomal subunit protein uL3
B2: Small ribosomal subunit protein uS15
C1: Ribosomal protein L4
C2: 18S rRNA
D1: Large ribosomal subunit protein eL31
E1: 60S ribosomal protein L32
F1: Large ribosomal subunit protein uL30
H1: Large ribosomal subunit protein uL29
H2: 40S ribosomal protein S21
I1: 60S ribosomal protein L36
J1: Ribosomal protein L37
J2: Small ribosomal subunit protein uS5
K1: Large ribosomal subunit protein eL38
K2: 40S ribosomal protein S8
L1: 60S ribosomal protein L13
L2: Small ribosomal subunit protein uS4
M1: Large ribosomal subunit protein eL14
M2: Small ribosomal subunit protein eS19
N1: Ribosomal protein L15
N2: Small ribosomal subunit protein uS14
O1: 60S ribosomal protein L36a
O2: 40S ribosomal protein S4
P1: Large ribosomal subunit protein uL22
P2: Small ribosomal subunit protein uS13
Q1: Ribosomal protein L18
R1: Ribosomal protein L19
S1: 60S ribosomal protein L18a
S2: Small ribosomal subunit protein uS9
T1: Large ribosomal subunit protein eL21
T2: 40S ribosomal protein S25
U1: Large ribosomal subunit protein eL22
U2: 40S ribosomal protein S7
V1: Large ribosomal subunit protein uL14
W1: Large ribosomal subunit protein eL24
W2: 40S ribosomal protein S6
X1: Large ribosomal subunit protein uL23
Y1: Ribosomal protein L26
Y2: Small ribosomal subunit protein uS17
Z1: 60S ribosomal protein L27
a1: Large ribosomal subunit protein uL2
b1: 60S ribosomal protein L29
d2: Small ribosomal subunit protein eS28
e1: Large ribosomal subunit protein eL34
f1: Large ribosomal subunit protein eL33
g1: Large ribosomal subunit protein eL43
g2: Small ribosomal subunit protein uS2
h1: Large ribosomal subunit protein uL18
i1: 5S rRNA
i2: Small ribosomal subunit protein eS17
j1: 5.8S rRNA
k1: Large ribosomal subunit protein uL6
l1: Large ribosomal subunit protein eL6
m1: 60S ribosomal protein L7a
m2: 40S ribosomal protein S24
n1: Large ribosomal subunit protein uL15
q2: Small ribosomal subunit protein uS10
r2: Small ribosomal subunit protein uS8
u2: Small ribosomal subunit protein uS7
w2: DNA-(apurinic or apyrimidinic site) lyase
x2: FAU ubiquitin like and ribosomal protein S30 fusion a
y2: Small ribosomal subunit protein uS12
z2: Ribosomal protein S10
k2: Small ribosomal subunit protein RACK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,389,392169
Polymers3,386,86877
Non-polymers2,52492
Water00
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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Large ribosomal subunit protein ... , 25 types, 25 molecules 1141718191B1D1F1H1K1M1P1T1U1V1W1X1a1e1f1g1h1k1l1n1

#1: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D2YXB7
#4: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 15558.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6NKG9
#8: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11


Mass: 20441.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZQ07
#10: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a


Mass: 23663.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8V316
#12: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12959.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8TZ47
#15: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3


Mass: 46187.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UTD6
#19: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14356.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZQ60
#21: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 28775.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8ABD9
#22: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14511.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8B8Q0
#27: 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) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8ABQ5
#31: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 15991.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AYS1
#37: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21409.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8V1N6
#43: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18676.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8VEW4
#45: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 14901.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D2XXT3
#47: 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) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8U9A9
#48: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 17769.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D3BML7
#50: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a


Mass: 17719.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D3BGY2
#54: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28127.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AEY7
#57: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13383.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZM90
#58: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a


Mass: 12526.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8B711
#59: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10297.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D2YM12
#61: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34154.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AJY4
#65: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21789.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UMU8
#66: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 29592.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8VJ69
#69: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a


Mass: 16585.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8VKP0

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Protein , 3 types, 3 molecules 21w2x2

#2: Protein Ubiquitin-ribosomal protein eL40 fusion protein


Mass: 14772.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7Z7U5
#73: Protein DNA-(apurinic or apyrimidinic site) lyase / 40S ribosomal protein S3


Mass: 27116.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle
References: UniProt: A0A1A8UXU3, DNA-(apurinic or apyrimidinic site) lyase
#74: Protein FAU ubiquitin like and ribosomal protein S30 fusion a / Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed


Mass: 14535.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UZP9

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40S ribosomal protein ... , 10 types, 10 molecules 3282A2H2K2O2T2U2W2m2

#3: Protein 40S ribosomal protein S27


Mass: 9508.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6PBA9
#11: Protein 40S ribosomal protein S26


Mass: 15669.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D2XVU3
#14: Protein 40S ribosomal protein S15


Mass: 17041.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AHB8
#23: Protein 40S ribosomal protein S21


Mass: 9217.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZU82
#28: Protein 40S ribosomal protein S8


Mass: 24077.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8V8I4
#36: Protein 40S ribosomal protein S4


Mass: 29669.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AV86
#44: Protein 40S ribosomal protein S25


Mass: 13856.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8A2D2
#46: Protein 40S ribosomal protein S7


Mass: 22271.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6M2W4
#49: Protein 40S ribosomal protein S6


Mass: 28697.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UHL8
#68: Protein 40S ribosomal protein S24


Mass: 15299.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6MIM3

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Small ribosomal subunit protein ... , 19 types, 19 molecules 425172B2J2L2M2N2P2S2Y2d2g2i2q2r2u2y2k2

#5: Protein Small ribosomal subunit protein eS1


Mass: 30143.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UD98
#6: Protein/peptide Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: Q6YLX4
#9: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UGY7
#16: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17217.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8A4M8
#26: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 30127.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UIW0
#30: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22585.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6MB21
#32: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16030.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8A9I2
#34: Protein Small ribosomal subunit protein uS14


Mass: 8726.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence refers to XP_015803583.2
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle
#38: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17772.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8U9P7
#42: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16361.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8A203
#52: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 18586.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8TZX7
#56: Protein Small ribosomal subunit protein eS28 / 40S ribosomal protein S28


Mass: 7838.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AHF9
#60: 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: 34531.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AVH6
#63: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15508.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AN05
#70: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13372.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AR50
#71: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14895.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6LFT6
#72: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 22842.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UE67
#75: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15885.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A9D2XSV1
#77: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor of activated protein kinase C


Mass: 35046.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8B6N7

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Ribosomal protein ... , 8 types, 8 molecules 61C1J1N1Q1R1Y1z2

#7: Protein Ribosomal protein L10


Mass: 24699.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8VG34
#17: Protein Ribosomal protein L4


Mass: 42553.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6NQ48
#25: Protein Ribosomal protein L37


Mass: 11110.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZT01
#33: Protein Ribosomal protein L15


Mass: 24196.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UDR0
#39: Protein Ribosomal protein L18


Mass: 21625.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8URP0
#40: Protein Ribosomal protein L19


Mass: 23494.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8U3R2
#51: Protein Ribosomal protein L26


Mass: 17254.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8U110
#76: Protein Ribosomal protein S10


Mass: 18993.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AVN4

-
RNA chain , 4 types, 4 molecules A1C2i1j1

#13: RNA chain 28S rRNA


Mass: 1302721.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: GenBank: EU780557
#18: RNA chain 18S rRNA


Mass: 592700.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: GenBank: EU780557
#62: RNA chain 5S rRNA


Mass: 38739.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: GenBank: 76360152
#64: RNA chain 5.8S rRNA


Mass: 51758.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: GenBank: EU780557

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60S ribosomal protein ... , 8 types, 8 molecules E1I1L1O1S1Z1b1m1

#20: Protein 60S ribosomal protein L32


Mass: 15832.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8VA16
#24: Protein 60S ribosomal protein L36


Mass: 12186.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZR96
#29: Protein 60S ribosomal protein L13


Mass: 24369.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8A6V0
#35: Protein 60S ribosomal protein L36a


Mass: 12565.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8TYD5
#41: Protein 60S ribosomal protein L18a


Mass: 20728.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UY99
#53: Protein 60S ribosomal protein L27


Mass: 15849.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UQB0
#55: Protein 60S ribosomal protein L29


Mass: 7479.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A8C6L745
#67: Protein 60S ribosomal protein L7a


Mass: 30091.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8U664

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Non-polymers , 2 types, 92 molecules

#78: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#79: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Young killifish ribosome / Type: RIBOSOME / Entity ID: #1-#65, #77, #66-#76 / Source: NATURAL
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMPotassium ChlorideKCl1
215 mMMagnesium ChlorideMgCl21
320 mMTris-hydrochlorideTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE
Details: Blot time 3 seconds Blot force 10 Wait time 30 seconds

-
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: 1000 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.41 sec. / Electron dose: 65.77 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 7785
EM imaging opticsEnergyfilter name: GIF Bioquantum / Details: BioQuantum K3 imaging filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.2.1particle selectiontemplate matching
2PHENIX1.21.2_5419model refinement
5cryoSPARC4.2.1CTF correction
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 919623
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.56 Å / Resolution method: OTHER / Num. of particles: 292135 / Details: Mean of focus-refined map's resolutions / Symmetry type: POINT
RefinementCross valid method: NONE

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