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- PDB-7oyb: Cryo-EM structure of the 6 hpf zebrafish embryo 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 7oyb
TitleCryo-EM structure of the 6 hpf zebrafish embryo 80S ribosome
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 28
  • (Ribosomal protein ...) x 15
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • ATPase H+ transporting V0 subunit e1
  • DNA-(apurinic or apyrimidinic site) lyase
  • Guanine nucleotide-binding protein subunit beta-2-like 1
  • Rpl41
  • Zgc:171772
KeywordsRIBOSOME / translation / embryo / zebrafish / maternal
Function / homology
Function and homology information


optokinetic behavior / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / TNFR1-induced NF-kappa-B signaling pathway / TNFR1-mediated ceramide production / : / : / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex ...optokinetic behavior / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / TNFR1-induced NF-kappa-B signaling pathway / TNFR1-mediated ceramide production / : / : / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / : / Protein methylation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mTORC1-mediated signalling / brain segmentation / Regulation of TNFR1 signaling / convergent extension involved in gastrulation / : / : / primitive hemopoiesis / embryonic retina morphogenesis in camera-type eye / anatomical structure development / hemoglobin biosynthetic process / mitochondrial cytochrome c oxidase assembly / chordate embryonic development / embryonic brain development / ribosomal subunit / exocrine pancreas development / positive regulation of gastrulation / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / definitive hemopoiesis / pancreas development / regulation of establishment of cell polarity / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of Wnt signaling pathway / regulation of innate immune response / regulation of cell division / erythrocyte maturation / hemopoiesis / intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mitochondrial respiratory chain complex I assembly / hematopoietic stem cell differentiation / protein-RNA complex assembly / vasculogenesis / erythrocyte development / translation regulator activity / rough endoplasmic reticulum / laminin binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / erythrocyte differentiation / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / regulation of erythrocyte differentiation / brain development / ribosomal large subunit assembly / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / rRNA processing / large ribosomal subunit / protein tag activity / regulation of protein localization / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / angiogenesis / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / regulation of cell cycle / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / metallochaperone-like domain / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S8e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S19 / 60S ribosomal protein L24 / 60S ribosomal protein L28 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S19 / 60S ribosomal protein L24 / 60S ribosomal protein L28 / Zgc:171772 / 60S ribosomal protein L14 / 40S ribosomal protein S23 / 40S ribosomal protein S24 / Ribosomal protein L22 / Ribosomal protein L23a / Guanine nucleotide-binding protein subunit beta-2-like 1 / 60S ribosomal protein L36a / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 40S ribosomal protein S16 / 60S ribosomal protein L13a / 60S ribosomal protein L32 / 60S ribosomal protein L31 / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S27 / 60S ribosomal protein L6 / 40S ribosomal protein S17 / Rpl3 protein / 60S ribosomal protein L9 / 40S ribosomal protein S4, X isoform / 60S ribosomal protein L18 / 60S ribosomal protein L29 / 60S ribosomal protein L38 / 60S ribosomal protein L35a / 40S ribosomal protein S6 / Ribosomal protein L15 / 40S ribosomal protein S13 / Ribosomal protein L39 / Ribosomal protein L5b / 60S ribosomal protein L11 / Ribosomal protein L37 / 60S ribosomal protein L21 / 40S ribosomal protein S2 / 60S ribosomal protein L8 / 60S ribosomal protein L27a / 60S ribosomal protein L19 / 40S ribosomal protein S9 / 40S ribosomal protein S26 / 40S ribosomal protein S20 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / Ribosomal protein S14 / 40S ribosomal protein S3a / 60S ribosomal protein L7a / FAU ubiquitin-like and ribosomal protein S30 fusion a / 60S ribosomal protein L23 / Ribosomal protein S5 / 60S ribosomal protein L36 / Ribosomal protein L7 / 40S ribosomal protein S29 / 40S ribosomal protein S15a / 40S ribosomal protein S15 / 60S ribosomal protein L26 / 40S ribosomal protein S10 / 60S ribosomal protein L17 / 40S ribosomal protein S21 / 60S ribosomal protein L30 / 40S ribosomal protein S11 / 60S ribosomal protein L27 / 60S ribosomal protein L10 / DNA-(apurinic or apyrimidinic site) lyase / 60S ribosomal protein L4 / 60S ribosomal protein L18a / 60S ribosomal protein L34 / 40S ribosomal protein SA / 40S ribosomal protein S18 / 60S ribosomal protein L35 / 60S ribosomal protein L13
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLeesch, F. / Lorenzo-Orts, L. / Grishkovskaya, I. / Kandolf, S. / Belacic, K. / Meinhart, A. / Haselbach, D. / Pauli, A.
Funding support Austria, Switzerland, 5items
OrganizationGrant numberCountry
Austrian Research Promotion AgencyFFG-852936 Austria
Austrian Science FundSTART Projekt Y 1031-B28 Austria
Austrian Science FundSFB RNA-Deco F 80 Austria
Swiss National Science FoundationP2GEP3_191204 Switzerland
European Molecular Biology Organization (EMBO)ALTF 1165-2019
CitationJournal: Nature / Year: 2023
Title: A molecular network of conserved factors keeps ribosomes dormant in the egg.
Authors: Friederike Leesch / Laura Lorenzo-Orts / Carina Pribitzer / Irina Grishkovskaya / Josef Roehsner / Anastasia Chugunova / Manuel Matzinger / Elisabeth Roitinger / Katarina Belačić / Susanne ...Authors: Friederike Leesch / Laura Lorenzo-Orts / Carina Pribitzer / Irina Grishkovskaya / Josef Roehsner / Anastasia Chugunova / Manuel Matzinger / Elisabeth Roitinger / Katarina Belačić / Susanne Kandolf / Tzi-Yang Lin / Karl Mechtler / Anton Meinhart / David Haselbach / Andrea Pauli /
Abstract: Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron ...Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
History
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
22: 18S rRNA
51: 28S rRNA
71: 5S rRNA
81: 5.8S rRNA
A1: 60S ribosomal protein L8
A2: 40S ribosomal protein SA
B1: Ribosomal protein L3
B2: 40S ribosomal protein S3a
C1: Ribosomal protein L4
C2: 40S ribosomal protein S2
D1: Ribosomal protein L5b
D2: DNA-(apurinic or apyrimidinic site) lyase
E1: 60S ribosomal protein L6
E2: 40S ribosomal protein S4, X isoform
F1: Ribosomal protein L7
F2: Ribosomal protein S5
G1: 60S ribosomal protein L7a
G2: 40S ribosomal protein S6
H1: 60S ribosomal protein L9
H2: 40S ribosomal protein S7
I1: 60S ribosomal protein L10
I2: 40S ribosomal protein S8
J1: 60S ribosomal protein L11
J2: 40S ribosomal protein S9
K2: Ribosomal protein S10
L1: 60S ribosomal protein L13
L2: 40S ribosomal protein S11
M1: 60S ribosomal protein L14
N1: Ribosomal protein L15
N2: 40S ribosomal protein S13
O1: 60S ribosomal protein L13a
O2: Ribosomal protein S14
P1: 60S ribosomal protein L17
P2: 40S ribosomal protein S15
Q1: Ribosomal protein L18
Q2: Ribosomal protein S16
R1: 60S ribosomal protein L19
R2: 40S ribosomal protein S17
S1: 60S ribosomal protein L18a
S2: 40S ribosomal protein S18
T1: 60S ribosomal protein L21
T2: 40S ribosomal protein S19
U1: Ribosomal protein L22
U2: 40S ribosomal protein S20
V1: 60S ribosomal protein L23
V2: 40S ribosomal protein S21
W1: 60S ribosomal protein L24
W2: 40S ribosomal protein S15a
X1: Ribosomal protein L23a
X2: 40S ribosomal protein S23
Y1: ATPase H+ transporting V0 subunit e1
Y2: 40S ribosomal protein S24
Z1: 60S ribosomal protein L27
Z2: 40S ribosomal protein S25
a1: 60S ribosomal protein L27a
a2: 40S ribosomal protein S26
b1: 60S ribosomal protein L29
b2: 40S ribosomal protein S27
c1: 60S ribosomal protein L30
c2: 40S ribosomal protein S28
d1: 60S ribosomal protein L31
d2: 40S ribosomal protein S29
e1: Ribosomal protein L32
e2: 40S ribosomal protein S30
f1: 60S ribosomal protein L35a
g1: 60S ribosomal protein L34
g2: Guanine nucleotide-binding protein subunit beta-2-like 1
h1: 60S ribosomal protein L35
i1: 60S ribosomal protein L36
j1: Ribosomal protein L37
k1: 60S ribosomal protein L38
l1: Ribosomal protein L39
m1: 60S ribosomal protein L40
n1: Rpl41
o1: 60S ribosomal protein L36a
p1: Zgc:171772
r1: 60S ribosomal protein L28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,501,228287
Polymers3,495,83777
Non-polymers5,392210
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules 22517181

#1: RNA chain 18S rRNA


Mass: 625968.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: GenBank: LR812041.1
#2: RNA chain 28S rRNA


Mass: 1382249.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: GenBank: AL935186.22
#3: RNA chain 5S rRNA


Mass: 38739.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: GenBank: LR812066.1
#4: RNA chain 5.8S rRNA


Mass: 50823.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: GenBank: LR812041.1

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60S ribosomal protein ... , 28 types, 28 molecules A1E1G1H1I1J1L1M1O1P1R1S1T1V1W1Z1a1b1c1d1f1g1h1i1k1m1o1r1

#5: Protein 60S ribosomal protein L8


Mass: 28131.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P0V6
#13: Protein 60S ribosomal protein L6


Mass: 30618.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q567N5
#17: Protein 60S ribosomal protein L7a


Mass: 30077.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PBZ1
#19: Protein 60S ribosomal protein L9


Mass: 21689.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q5BKV9
#21: Protein 60S ribosomal protein L10 / Protein QM / Ribosomal protein L10


Mass: 24664.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZV96
#23: Protein 60S ribosomal protein L11


Mass: 20415.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IQI6
#26: Protein 60S ribosomal protein L13


Mass: 24426.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q90Z10
#28: Protein 60S ribosomal protein L14


Mass: 16166.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A8E526
#31: Protein 60S ribosomal protein L13a


Mass: 23731.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q1LYB7
#33: Protein 60S ribosomal protein L17


Mass: 21476.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7T1K0
#37: Protein 60S ribosomal protein L19


Mass: 23522.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P5L3
#39: Protein 60S ribosomal protein L18a


Mass: 20725.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZWJ4
#41: Protein 60S ribosomal protein L21


Mass: 18574.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IQQ0
#45: Protein 60S ribosomal protein L23


Mass: 14908.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PC14
#47: Protein 60S ribosomal protein L24


Mass: 17929.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A0A0R4IMS3
#53: Protein 60S ribosomal protein L27


Mass: 15819.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZV82
#55: Protein 60S ribosomal protein L27a


Mass: 16621.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P2M0
#57: Protein 60S ribosomal protein L29


Mass: 7596.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DGL4
#59: Protein 60S ribosomal protein L30


Mass: 13004.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZUG6
#61: Protein 60S ribosomal protein L31


Mass: 14369.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q24JV3
#65: Protein 60S ribosomal protein L35a


Mass: 12503.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DGM0
#66: Protein 60S ribosomal protein L34


Mass: 13401.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZWJ7
#68: Protein 60S ribosomal protein L35


Mass: 14470.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q8JHJ1
#69: Protein 60S ribosomal protein L36


Mass: 12216.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6Q415
#71: Protein 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DGL9
#73: Protein 60S ribosomal protein L40 / CEP52 / Ubiquitin / Ubiquitin-60S ribosomal protein L40


Mass: 14786.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q3B7P7
#75: Protein 60S ribosomal protein L36a


Mass: 12565.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: P61485
#77: Protein 60S ribosomal protein L28


Mass: 15661.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A0A286YBP4

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40S ribosomal protein ... , 25 types, 25 molecules A2B2C2E2G2H2I2J2L2N2P2R2S2T2U2V2W2X2Y2Z2a2b2c2d2e2

#6: Protein 40S ribosomal protein SA / 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: 34043.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q803F6
#8: Protein 40S ribosomal protein S3a


Mass: 30256.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PBY1
#10: Protein 40S ribosomal protein S2


Mass: 30342.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6NWC3
#14: Protein 40S ribosomal protein S4, X isoform


Mass: 29746.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q642H9
#18: Protein 40S ribosomal protein S6


Mass: 28778.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DHL6
#20: Protein 40S ribosomal protein S7


Mass: 22293.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: P62084
#22: Protein 40S ribosomal protein S8


Mass: 24151.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: P62247
#24: Protein 40S ribosomal protein S9


Mass: 22515.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P5M3
#27: Protein 40S ribosomal protein S11


Mass: 18444.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZV05
#30: Protein 40S ribosomal protein S13


Mass: 17231.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IMW6
#34: Protein 40S ribosomal protein S15


Mass: 17040.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6Q421
#38: Protein 40S ribosomal protein S17


Mass: 15481.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q5BJA1
#40: Protein 40S ribosomal protein S18


Mass: 17772.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q8JGS9
#42: Protein 40S ribosomal protein S19


Mass: 15971.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A0A0R4IJ49
#44: Protein 40S ribosomal protein S20


Mass: 13315.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P6E7
#46: Protein 40S ribosomal protein S21


Mass: 8915.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZUG5
#48: Protein 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6Q420
#50: Protein 40S ribosomal protein S23


Mass: 15885.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A8KB78
#52: Protein 40S ribosomal protein S24


Mass: 15383.306 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: B7ZD34
#54: Protein 40S ribosomal protein S25


Mass: 13894.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PBI5
#56: Protein 40S ribosomal protein S26


Mass: 13053.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P6E2
#58: Protein 40S ribosomal protein S27


Mass: 9550.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q4VBV2
#60: Protein 40S ribosomal protein S28


Mass: 7838.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PBK3
#62: Protein 40S ribosomal protein S29


Mass: 6692.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6Q419
#64: Protein 40S ribosomal protein S30


Mass: 14651.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PC01

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Ribosomal protein ... , 15 types, 15 molecules B1C1D1F1F2K2N1O2Q1Q2U1X1e1j1l1

#7: Protein Ribosomal protein L3 / Rpl3 protein


Mass: 46358.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q5BJJ2
#9: Protein Ribosomal protein L4


Mass: 42644.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZW95
#11: Protein Ribosomal protein L5b


Mass: 34118.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IQB1
#15: Protein Ribosomal protein L7


Mass: 28505.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6Q417
#16: Protein Ribosomal protein S5


Mass: 22909.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PC80
#25: Protein Ribosomal protein S10


Mass: 18919.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7T1J9
#29: Protein Ribosomal protein L15


Mass: 24124.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DHS3
#32: Protein Ribosomal protein S14


Mass: 16274.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PBW3
#35: Protein Ribosomal protein L18 / Zgc:92872 / Zgc:92872 protein


Mass: 21045.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DGL0
#36: Protein Ribosomal protein S16 / Rps16 protein


Mass: 16387.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q1LWH1
#43: Protein Ribosomal protein L22


Mass: 16316.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: F1QG80
#49: Protein Ribosomal protein L23a


Mass: 17686.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: F1QGI3
#63: Protein Ribosomal protein L32 / Zgc:136952


Mass: 15851.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q24JV1
#70: Protein Ribosomal protein L37


Mass: 11074.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IQJ7
#72: Protein/peptide Ribosomal protein L39 / Zgc:92371


Mass: 6279.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IMW8

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Protein , 4 types, 4 molecules D2Y1g2p1

#12: Protein DNA-(apurinic or apyrimidinic site) lyase


Mass: 26879.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish)
References: UniProt: Q7ZVD9, DNA-(apurinic or apyrimidinic site) lyase
#51: Protein ATPase H+ transporting V0 subunit e1 / Ribosomal protein L26 / Rpl26 protein


Mass: 17387.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7SXA1
#67: Protein Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor of activated protein kinase C / RACK


Mass: 35161.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: O42248
#76: Protein Zgc:171772 / Zgc:171772 protein


Mass: 10229.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A7YY10

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Protein/peptide , 1 types, 1 molecules n1

#74: Protein/peptide Rpl41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish)

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Non-polymers , 2 types, 210 molecules

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


Mass: 24.305 Da / Num. of mol.: 203 / Source method: obtained synthetically / Formula: Mg
#79: 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

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Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 80S ribosome from 6 hpf zebrafish embryos / Type: RIBOSOME / Entity ID: #1-#77 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Danio rerio (zebrafish) / Tissue: 6 hpf embryos
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2100 mMpotassium chlorideKCl1
35 mMmagnesium acetateMg(OAc)21
41 mMdithiothreitolDTT1
520 mMammonium chlorideNH4Cl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 70 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.3 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11860

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Processing

SoftwareName: UCSF ChimeraX / Version: 0.91/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
1cryoSPARC2.14particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC2.14initial Euler assignment
10cryoSPARC2.14final Euler assignment
11cryoSPARCclassification
12cryoSPARC2.143D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1285670
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 775288 / Details: composite map of separately refined subunits / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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