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- PDB-7oyc: Cryo-EM structure of the Xenopus egg 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 7oyc
TitleCryo-EM structure of the Xenopus egg 80S ribosome
Components
  • (40S ribosomal protein ...) x 26
  • (60S ribosomal protein ...) x 27
  • (Ribosomal protein ...) x 2
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DNA-(apurinic or apyrimidinic site) lyase
  • Death-associated protein-like 1-B
  • Eef2-prov protein
  • Eukaryotic translation initiation factor 5A
  • Gnb2l1-prov protein
  • HABP4_PAI-RBP1 domain-containing protein
  • KOW domain-containing protein
  • MGC116452 protein
  • MGC130910 protein
  • MGC85428 protein
  • Ribosomal_L16 domain-containing protein
  • Ribosomal_L18e/L15P domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • Ribosomal_S7 domain-containing protein
  • Rpl3-prov protein
  • Rpl32
  • Rpl37a
  • Rpl41
  • Rpl5-b protein
  • Rps14
  • Rps16 protein
  • TRASH domain-containing protein
KeywordsRIBOSOME / Eif5a / Eef2 / Habp4 / DapL1 / Dap1 / egg / Xenopus
Function / homology
Function and homology information


death domain binding / positive regulation of translational termination / ribosome hibernation / positive regulation of translational elongation / ribosomal subunit / laminin receptor activity / translational elongation / 90S preribosome / translation elongation factor activity / protein-RNA complex assembly ...death domain binding / positive regulation of translational termination / ribosome hibernation / positive regulation of translational elongation / ribosomal subunit / laminin receptor activity / translational elongation / 90S preribosome / translation elongation factor activity / protein-RNA complex assembly / rough endoplasmic reticulum / laminin binding / translation regulator activity / translation repressor activity / translation initiation factor binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of autophagy / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / apoptotic signaling pathway / spindle / rRNA processing / kinase activity / ribosome biogenesis / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / centrosome / endoplasmic reticulum membrane / GTP binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DAP1/DAPL1 / Death-associated protein / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Ribosomal protein L14, KOW motif / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold ...DAP1/DAPL1 / Death-associated protein / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Ribosomal protein L14, KOW motif / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Ribosomal protein S14, type Z, archaeal / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal L15/L27a, N-terminal / Elongation factor G C-terminus / Ribosomal protein L28e / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L23 / EF-G domain III/V-like / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / : / Ribosomal protein S17e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S27 / Large ribosomal subunit protein uL13 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S27 / Large ribosomal subunit protein uL13 / 40S ribosomal protein S29 / 60S ribosomal protein L10 / Small ribosomal subunit protein uS7 / Ribosomal_L18e/L15P domain-containing protein / Ribosomal protein L15 / Large ribosomal subunit protein eL14 / 60S ribosomal protein L32 / KOW domain-containing protein / 60S ribosomal protein L37a isoform X3 / Large ribosomal subunit protein uL23 / 60S ribosomal protein L8 / Large ribosomal subunit protein eL24 / HABP4_PAI-RBP1 domain-containing protein / 60S ribosomal protein L9 / Large ribosomal subunit protein eL34 / Ribosomal protein L37 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS19 / Death-associated protein-like 1.S / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS24 / Large ribosomal subunit protein uL4B / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL29 / MGC116435 protein / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL36 / 60S ribosomal protein L36a isoform X1 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL28 / 60S ribosomal protein L29 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein eS21 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS12 / 60S ribosomal protein L6 / 40S ribosomal protein S8 / 40S ribosomal protein S25 / 60S ribosomal protein L13 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL14 / 60S ribosomal protein L21 / 60S ribosomal protein L7a / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL31 / 60S ribosomal protein L27 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L18a / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS2 / Eukaryotic translation initiation factor 5A-1 / Elongation factor 2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL19 / DNA-(apurinic or apyrimidinic site) lyase / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS1A / 60S ribosomal protein L5-B / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
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 20, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 6, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
11: Eukaryotic translation initiation factor 5A
22: 18S rRNA
51: 28S rRNA
71: 5S rRNA
81: 5.8S rRNA
A1: 60S ribosomal protein L8
A2: 40S ribosomal protein SA
B1: Rpl3-prov protein
B2: 40S ribosomal protein S3a-A
C1: 60S ribosomal protein L4-B
C2: 40S ribosomal protein S2
D1: Rpl5-b protein
D2: DNA-(apurinic or apyrimidinic site) lyase
E1: 60S ribosomal protein L6
E2: 40S ribosomal protein S4
F1: MGC130910 protein
F2: Ribosomal_S7 domain-containing protein
G1: 60S ribosomal protein L7a
G2: 40S ribosomal protein S6
H1: 60S ribosomal protein L9
H2: 40S ribosomal protein S7
I1: Ribosomal_L16 domain-containing protein
I2: 40S ribosomal protein S8
J1: 60S ribosomal protein L11
J2: 40S ribosomal protein S9
K2: 40S 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: Rps14
P1: 60S ribosomal protein L17
P2: 40S ribosomal protein S15
Q1: Ribosomal_L18e/L15P domain-containing protein
Q2: Rps16 protein
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: 60S ribosomal protein L22
U2: 40S ribosomal protein S20
V1: 60S ribosomal protein L23
V2: 40S ribosomal protein S21
W1: TRASH domain-containing protein
W2: 40S ribosomal protein S15a
X1: Ribosomal_L23eN domain-containing protein
X2: 40S ribosomal protein S23
Y1: KOW domain-containing protein
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: Rpl32
e2: 40S ribosomal protein S30
f1: 60S ribosomal protein L35a
g1: 60S ribosomal protein L34
g2: Gnb2l1-prov protein
h1: 60S ribosomal protein L35
i1: 60S ribosomal protein L36
i2: HABP4_PAI-RBP1 domain-containing protein
j1: Ribosomal protein L37
k1: 60S ribosomal protein L38
l1: MGC116452 protein
m1: 60S ribosomal protein L40
n1: Rpl41
o1: MGC85428 protein
p1: Rpl37a
r1: 60S ribosomal protein L28
s1: Death-associated protein-like 1-B
v2: Eef2-prov protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,587,981222
Polymers3,584,26681
Non-polymers3,715141
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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Protein , 21 types, 21 molecules 11B1D1D2F1F2I1O2Q1Q2W1X1Y1e1g2i2l1o1p1s1v2

#1: Protein Eukaryotic translation initiation factor 5A / eIF-5A


Mass: 16813.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7ZXG3
#8: Protein Rpl3-prov protein


Mass: 46144.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7ZYR1
#12: Protein Rpl5-b protein


Mass: 34066.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q8AVI7
#13: Protein DNA-(apurinic or apyrimidinic site) lyase


Mass: 27026.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg
References: UniProt: Q7ZYT3, DNA-(apurinic or apyrimidinic site) lyase
#16: Protein MGC130910 protein


Mass: 28762.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q3B8I3
#17: Protein Ribosomal_S7 domain-containing protein


Mass: 22780.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8F8E2
#22: Protein Ribosomal_L16 domain-containing protein


Mass: 24634.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8F5F1
#33: Protein Rps14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg
#36: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 21659.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8FN04
#37: Protein Rps16 protein


Mass: 16361.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q3KQC9
#48: Protein TRASH domain-containing protein


Mass: 17721.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8HGE0
#50: Protein Ribosomal_L23eN domain-containing protein


Mass: 17718.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8H4S4
#52: Protein KOW domain-containing protein


Mass: 17235.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8GXU8
#64: Protein Rpl32


Mass: 15818.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8GHL2
#68: Protein Gnb2l1-prov protein / LOC446289 protein


Mass: 35107.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q8AVP6
#71: Protein HABP4_PAI-RBP1 domain-containing protein


Mass: 42746.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8HPG3
#74: Protein MGC116452 protein / MGC116477 protein


Mass: 6398.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q4FZP7
#77: Protein MGC85428 protein


Mass: 12496.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q66KU5
#78: Protein Rpl37a


Mass: 10283.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8H102
#80: Protein Death-associated protein-like 1-B


Mass: 12548.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A3KMU5
#81: Protein Eef2-prov protein


Mass: 95552.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Eggs / References: UniProt: Q7ZXP8

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RNA chain , 4 types, 4 molecules 22517181

#2: RNA chain 18S rRNA


Mass: 588678.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: GenBank: X04025.1
#3: RNA chain 28S rRNA


Mass: 1333067.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: GenBank: X59734.1
#4: RNA chain 5S rRNA


Mass: 38682.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: GenBank: M10635.1
#5: RNA chain 5.8S rRNA


Mass: 50198.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: GenBank: X02995.1

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60S ribosomal protein ... , 27 types, 27 molecules A1C1E1G1H1J1L1M1O1P1R1S1T1U1V1Z1a1b1c1d1f1g1h1i1k1m1r1

#6: Protein 60S ribosomal protein L8


Mass: 27980.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8H6H2
#10: Protein 60S ribosomal protein L4-B / L1B


Mass: 45525.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P02385
#14: Protein 60S ribosomal protein L6


Mass: 29743.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6DJF7
#18: Protein 60S ribosomal protein L7a


Mass: 29939.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6GQB2
#20: Protein 60S ribosomal protein L9


Mass: 21934.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8HTS7
#24: Protein 60S ribosomal protein L11


Mass: 20215.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q66KY6
#27: Protein 60S ribosomal protein L13


Mass: 24257.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6DJN5
#29: Protein 60S ribosomal protein L14


Mass: 16174.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8FWH1
#32: Protein 60S ribosomal protein L13a


Mass: 26450.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8ENM5
#34: Protein 60S ribosomal protein L17


Mass: 21457.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8I3J8
#38: Protein 60S ribosomal protein L19


Mass: 23550.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7ZYS1
#40: Protein 60S ribosomal protein L18a


Mass: 20697.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7SZB7
#42: Protein 60S ribosomal protein L21


Mass: 18706.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6GP41
#44: Protein 60S ribosomal protein L22


Mass: 14842.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P50886
#46: Protein 60S ribosomal protein L23


Mass: 14878.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6GNH1
#54: Protein 60S ribosomal protein L27


Mass: 15864.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6PHL5
#56: Protein 60S ribosomal protein L27a


Mass: 16636.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7SZB2
#58: Protein 60S ribosomal protein L29


Mass: 8596.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q66KW1
#60: Protein 60S ribosomal protein L30


Mass: 12959.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7SZC0
#62: Protein 60S ribosomal protein L31


Mass: 14548.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6NUH0
#66: Protein 60S ribosomal protein L35a / L32


Mass: 12630.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P02434
#67: Protein 60S ribosomal protein L34


Mass: 13325.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8HUR4
#69: Protein 60S ribosomal protein L35


Mass: 14492.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q4FZQ7
#70: Protein 60S ribosomal protein L36


Mass: 12362.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q66KU4
#73: Protein 60S ribosomal protein L38


Mass: 8226.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q66KV2
#75: Protein 60S ribosomal protein L40 / CEP52 / Ubiquitin / Ubiquitin-60S ribosomal protein L40


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6GQF3
#79: Protein 60S ribosomal protein L28


Mass: 15587.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q66KV6

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40S ribosomal protein ... , 26 types, 26 molecules A2B2C2E2G2H2I2J2K2L2N2P2R2S2T2U2V2W2X2Y2Z2a2b2c2d2e2

#7: 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: 34027.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7ZX07
#9: Protein 40S ribosomal protein S3a-A


Mass: 29998.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q801S3
#11: Protein 40S ribosomal protein S2


Mass: 30326.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7T0R9
#15: Protein 40S ribosomal protein S4


Mass: 29722.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P49401
#19: Protein 40S ribosomal protein S6


Mass: 28778.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7ZYU0
#21: Protein 40S ribosomal protein S7 / 40S ribosomal protein S8


Mass: 22226.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P02362
#23: Protein 40S ribosomal protein S8


Mass: 24109.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6DJI0
#25: Protein 40S ribosomal protein S9


Mass: 22627.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7ZYU4
#26: Protein 40S ribosomal protein S10


Mass: 18918.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q07254
#28: Protein 40S ribosomal protein S11


Mass: 18428.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q7SZ77
#31: Protein 40S ribosomal protein S13


Mass: 17287.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P49393
#35: Protein 40S ribosomal protein S15 / RIG protein


Mass: 17010.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P20342
#39: Protein 40S ribosomal protein S17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6GNF4
#41: Protein 40S ribosomal protein S18


Mass: 17717.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6NTT2
#43: Protein 40S ribosomal protein S19


Mass: 16079.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A310TRG4
#45: Protein 40S ribosomal protein S20 / S22


Mass: 13381.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P23403
#47: Protein 40S ribosomal protein S21


Mass: 9227.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6AZJ9
#49: Protein 40S ribosomal protein S15a


Mass: 14881.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q4QR44
#51: Protein 40S ribosomal protein S23


Mass: 15803.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6AZL9
#53: Protein 40S ribosomal protein S24 / S19


Mass: 15324.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: P02377
#55: Protein 40S ribosomal protein S25


Mass: 13863.302 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6DJJ1
#57: Protein 40S ribosomal protein S26


Mass: 13125.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q6AZL7
#59: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8EJM5
#61: Protein 40S ribosomal protein S28


Mass: 7852.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q66KP7
#63: Protein 40S ribosomal protein S29


Mass: 10202.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8F058
#65: Protein 40S ribosomal protein S30


Mass: 14537.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: Q4KLF0

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Ribosomal protein ... , 2 types, 2 molecules N1j1

#30: Protein Ribosomal protein L15


Mass: 24119.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8FRG2
#72: Protein Ribosomal protein L37


Mass: 11030.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg / References: UniProt: A0A1L8I2F1

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Protein/peptide , 1 types, 1 molecules n1

#76: Protein/peptide Rpl41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg

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Non-polymers , 2 types, 141 molecules

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


Mass: 24.305 Da / Num. of mol.: 134 / Source method: obtained synthetically / Formula: Mg
#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 interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Xenopus egg 80S ribosome / Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog) / Tissue: Egg
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMMagnesium acetateMg(OAc)21
220 mMHEPES1
3100 mMpotassium cholrideKCl1
41 mMDithiotreitolDTT1
510 mMammonium cholrideNH4Cl1
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
VitrificationCryogen name: ETHANE

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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 / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1

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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
2EPUimage acquisition
4CTFFIND4CTF correction
10cryoSPARC2.14initial Euler assignment
11cryoSPARC2.14final Euler assignment
12cryoSPARC2.14classification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412340 / Symmetry type: POINT

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