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- PDB-9eho: Octopus ribosome, hybrid 80S -

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Basic information

Entry
Database: PDB / ID: 9eho
TitleOctopus ribosome, hybrid 80S
Components
  • (40S ribosomal protein ...) x 14
  • (60S ribosomal protein ...) x 9
  • (Large ribosomal subunit protein ...) x 27
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 14
  • (tRNA) x 2
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Plectin/eS10 N-terminal domain-containing protein
  • RNA (5'-R(P*AP*CP*CP*AP*AP*AP*AP*AP*CP*C)-3')
  • Ribosomal S5
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • eL38
  • eS30
  • eS32
KeywordsRIBOSOME / Octopus ribosone
Function / homology
Function and homology information


90S preribosome / rough endoplasmic reticulum / positive regulation of apoptotic signaling pathway / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / structural constituent of chromatin / nucleosome ...90S preribosome / rough endoplasmic reticulum / positive regulation of apoptotic signaling pathway / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / structural constituent of chromatin / nucleosome / nucleosome assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / DNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Linker histone H1/H5 / Ribosomal protein L30e / metallochaperone-like domain / TRASH domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily ...: / Linker histone H1/H5 / Ribosomal protein L30e / metallochaperone-like domain / TRASH domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L30e signature 1. / Ribosomal protein S25 / S25 ribosomal protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / : / : / Ribosomal protein S7e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L7A/L8 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / : / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L35A superfamily / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / : / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / 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 S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S8e / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L8/Nhp2 family
Similarity search - Domain/homology
SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / : / : ...SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / 40S ribosomal protein S8 / 60S ribosomal protein L11 / 60S ribosomal protein L18a / Uncharacterized protein LOC115210796 / Ribosomal protein L19 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S25 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS13 / 40S ribosomal protein S15a / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL30 / 40S ribosomal protein S21 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS17 / 60S ribosomal protein L32 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL22 / 60S ribosomal protein L7a / 40S ribosomal protein S4 / 40S ribosomal protein S3 / Ribosomal S5 / 40S ribosomal protein S14a / Large ribosomal subunit protein eL33 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS4
Similarity search - Component
Biological speciesOctopus (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGao, J. / Yip, M.C.J. / Han, R. / Grearson, A. / Shao, S. / Lee, A.S.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
CitationJournal: bioRxiv / Year: 2026
Title: Evolution of a core ribosomal innovation in octopus.
Authors: Rishav Mitra / Richard Han / Trey J Scott / Anik G Grearson / Jessica A Willi / Christina G Liu / Hyeongju Kim / Michael C Jewett / Nicholas W Bellono / Amy Sy Lee /
Abstract: Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations in other steps of the central dogma. Octopuses exhibit complex nervous systems and ...Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations in other steps of the central dogma. Octopuses exhibit complex nervous systems and sophisticated behaviors that rival vertebrates, but via an entirely divergent evolutionary history. Here, we serendipitously discovered that octopus ribosomes contain a structural break in the core ribosomal RNA that is unique among all animals. This break site enhances translation fidelity to reduce miscoding and subsequent protein aggregation, even when engineered into evolutionarily distant bacterial ribosomes. Furthermore, high fidelity translation by octopus ribosomes supports proteomic stability during extensive RNA editing observed in cephalopods, suggesting synergy between distinct non-canonical modes of gene regulation. This adaptation emerged in recently derived octopuses with expanded nervous systems, thereby revealing a mechanism that could broadly support the evolution of novel organismal traits.
History
DepositionNov 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
5: 28S rRNA
7: 5S rRNA
8: 5.8S rRNA
A: Large ribosomal subunit protein uL2
B: 60S ribosomal protein L3
I: Large ribosomal subunit protein uL16
P: Large ribosomal subunit protein uL22
Q: Large ribosomal subunit protein uL15/eL18 domain-containing protein
V: Large ribosomal subunit protein uL14
a: Large ribosomal subunit protein uL15
e: 60S ribosomal protein L32
g: Large ribosomal subunit protein eL34
j: Ribosomal protein L37
m: Ubiquitin-ribosomal protein eL40 fusion protein
o: Large ribosomal subunit protein eL42
p: Large ribosomal subunit protein eL43
C: Large ribosomal subunit protein uL4 C-terminal domain-containing protein
D: Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein
E: Large ribosomal subunit protein eL6
F: 60S ribosomal protein L7 isoform X1
G: 60S ribosomal protein L7a
H: Large ribosomal subunit protein uL6
J: 60S ribosomal protein L11
L: Large ribosomal subunit protein eL13
M: Large ribosomal subunit protein eL14
N: Ribosomal protein L15
O: Large ribosomal subunit protein uL13
R: Ribosomal protein L19
S: 60S ribosomal protein L18a
T: 60S ribosomal protein L21
U: Large ribosomal subunit protein eL22
W: Large ribosomal subunit protein eL24
X: Large ribosomal subunit protein uL23 N-terminal domain-containing protein
Y: Large ribosomal subunit protein uL24
Z: Large ribosomal subunit protein eL27
b: 60S ribosomal protein L29
c: Large ribosomal subunit protein eL30
d: Large ribosomal subunit protein eL31
f: Large ribosomal subunit protein eL33
h: 60S ribosomal protein L35
i: Large ribosomal subunit protein eL36
k: eL38
l: Large ribosomal subunit protein eL39
r: Large ribosomal subunit protein eL28
n: eS32
AA: 18S rRNA
aa: 40S ribosomal protein S25
bb: 40S ribosomal protein S26
BB: Small ribosomal subunit protein uS2
ee: Small ribosomal subunit protein uS14
CC: Small ribosomal subunit protein eS1
cc: 40S ribosomal protein S27
DD: Small ribosomal subunit protein uS5
dd: Small ribosomal subunit protein eS28
EE: 40S ribosomal protein S3
FF: 40S ribosomal protein S4
ff: eS30
GG: Ribosomal S5
HH: Small ribosomal subunit protein eS6
hh: Small ribosomal subunit protein RACK1
II: 40S ribosomal protein S7
JJ: 40S ribosomal protein S8
KK: Small ribosomal subunit protein uS4
LL: Plectin/eS10 N-terminal domain-containing protein
MM: 40S ribosomal protein S11
OO: Small ribosomal subunit protein uS15
PP: 40S ribosomal protein S14a
QQ: Small ribosomal subunit protein uS19
RR: 40S ribosomal protein S16
SS: Small ribosomal subunit protein eS17
TT: Small ribosomal subunit protein uS13
UU: 40S ribosomal protein S19
VV: Small ribosomal subunit protein uS10
WW: 40S ribosomal protein S21
XX: 40S ribosomal protein S15a
YY: Small ribosomal subunit protein uS12
ZZ: 40S ribosomal protein S24
2: tRNA
3: tRNA
1: RNA (5'-R(P*AP*CP*CP*AP*AP*AP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,287,249293
Polymers4,281,66380
Non-polymers5,586213
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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RNA chain , 7 types, 7 molecules 578AA231

#1: RNA chain 28S rRNA


Mass: 1674451.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)
#2: RNA chain 5S rRNA


Mass: 38239.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: GenBank: 1697376669
#3: RNA chain 5.8S rRNA


Mass: 51901.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)
#46: RNA chain 18S rRNA


Mass: 962557.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)
#78: RNA chain tRNA


Mass: 24439.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)
#79: RNA chain tRNA


Mass: 23630.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)
#80: RNA chain RNA (5'-R(P*AP*CP*CP*AP*AP*AP*AP*AP*CP*C)-3')


Mass: 3151.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)

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Large ribosomal subunit protein ... , 27 types, 27 molecules AIPQVagopCDEHLMOUWXYZcdfilr

#4: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28372.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HBD8
#6: Protein Large ribosomal subunit protein uL16 / 60S ribosomal protein L10


Mass: 25299.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GH20
#7: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21676.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FWK7
#8: Protein Large ribosomal subunit protein uL15/eL18 domain-containing protein


Mass: 21665.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GH52
#9: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23


Mass: 14759.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SHL5
#10: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a


Mass: 16978.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GUZ8
#12: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SDP0
#15: Protein Large ribosomal subunit protein eL42


Mass: 12527.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8H955
#16: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10250.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FTQ7
#17: Protein Large ribosomal subunit protein uL4 C-terminal domain-containing protein


Mass: 54810.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8I1Q2
#18: Protein Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein


Mass: 34344.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GVI8
#19: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 32395.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HB73
#22: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21256.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GSW6
#24: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 24775.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HYP5
#25: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 17796.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HPP0
#27: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a


Mass: 23563.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8ICA5
#31: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 15865.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7TBZ9
#32: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 18118.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7T9B6
#33: Protein Large ribosomal subunit protein uL23 N-terminal domain-containing protein


Mass: 22882.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HCQ3
#34: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 16866.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HTW6
#35: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 16198.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HEV7
#37: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12842.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SRS2
#38: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14433.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FL34
#39: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a


Mass: 14928.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0AA36B3M9
#41: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 13262.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8G079
#43: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6319.710 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GH95
#44: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 15691.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8IE99

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60S ribosomal protein ... , 9 types, 9 molecules BeFGJSTbh

#5: Protein 60S ribosomal protein L3


Mass: 46218.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GUX3
#11: Protein 60S ribosomal protein L32


Mass: 15925.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7T6K0
#20: Protein 60S ribosomal protein L7 isoform X1


Mass: 39385.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SRC5
#21: Protein 60S ribosomal protein L7a


Mass: 30368.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7TFK4
#23: Protein 60S ribosomal protein L11 / Ribosomal L11


Mass: 20770.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7S926
#29: Protein 60S ribosomal protein L18a


Mass: 20936.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SAY7
#30: Protein 60S ribosomal protein L21


Mass: 18470.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HKY0
#36: Protein 60S ribosomal protein L29


Mass: 10729.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8G2J8
#40: Protein 60S ribosomal protein L35


Mass: 14678.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GA56

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Ribosomal protein ... , 3 types, 3 molecules jNR

#13: Protein Ribosomal protein L37


Mass: 11615.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GUF0
#26: Protein Ribosomal protein L15


Mass: 24144.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FH14
#28: Protein Ribosomal protein L19


Mass: 23470.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SCW8

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Protein , 5 types, 5 molecules mkffGGLL

#14: Protein Ubiquitin-ribosomal protein eL40 fusion protein


Mass: 14389.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8IFH5
#42: Protein eL38


Mass: 12091.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)
#57: Protein eS30


Mass: 19686.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SBH5
#58: Protein Ribosomal S5


Mass: 23012.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0AA36AJI8
#64: Protein Plectin/eS10 N-terminal domain-containing protein


Mass: 17844.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GNG4

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Protein/peptide , 1 types, 1 molecules n

#45: Protein/peptide eS32


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata)

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40S ribosomal protein ... , 14 types, 14 molecules aabbccEEFFIIJJMMPPRRUUWWXXZZ

#47: Protein 40S ribosomal protein S25


Mass: 13193.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SED9
#48: Protein 40S ribosomal protein S26


Mass: 13419.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HXQ8
#52: Protein 40S ribosomal protein S27


Mass: 9498.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HUU3
#55: Protein 40S ribosomal protein S3


Mass: 26894.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A7E6FAP0
#56: Protein 40S ribosomal protein S4


Mass: 30057.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7TL90
#61: Protein 40S ribosomal protein S7


Mass: 22503.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0AA36BFQ8
#62: Protein 40S ribosomal protein S8


Mass: 24049.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7S8V1
#65: Protein 40S ribosomal protein S11


Mass: 18270.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0AA36BFS1
#67: Protein 40S ribosomal protein S14a


Mass: 16221.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0AA36AUI4
#69: Protein 40S ribosomal protein S16


Mass: 16754.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SLL6
#72: Protein 40S ribosomal protein S19


Mass: 17619.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8H8L5
#74: Protein 40S ribosomal protein S21


Mass: 9084.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SVZ2
#75: Protein 40S ribosomal protein S15a / Ribosomal S15Aa


Mass: 14815.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SI58
#77: Protein 40S ribosomal protein S24


Mass: 15354.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SEH2

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Small ribosomal subunit protein ... , 14 types, 14 molecules BBeeCCDDddHHhhKKOOQQSSTTVVYY

#49: Protein Small ribosomal subunit protein uS2


Mass: 32683.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8HYK6
#50: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6682.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FZK2
#51: Protein Small ribosomal subunit protein eS1


Mass: 29796.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GKW9
#53: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 30003.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FIV1
#54: Protein Small ribosomal subunit protein eS28 / 40S ribosomal protein S28


Mass: 7593.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FIY8
#59: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6


Mass: 85150.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FU76
#60: Protein Small ribosomal subunit protein RACK1


Mass: 35185.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8FPF8
#63: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22436.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0AA36EZW4
#66: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17326.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8G2L9
#68: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15


Mass: 17647.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8GTJ3
#70: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15465.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7T0R9
#71: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17780.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SHR0
#73: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13477.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A0L8IH34
#76: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15977.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Octopus (invertebrata) / References: UniProt: A0A6P7SY84

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Non-polymers , 3 types, 213 molecules

#81: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 205 / Source method: obtained synthetically / Formula: Mg
#82: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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: Octopus ribosome, hybrid state / Type: RIBOSOME / Entity ID: #1-#80 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Octopus (invertebrata)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15061 / Symmetry type: POINT

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