[English] 日本語
Yorodumi
- PDB-7oyb: Cryo-EM structure of the 6 hpf zebrafish embryo 80S ribosome -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of mRNA cis splicing, via spliceosome / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / SCF-beta-TrCP mediated degradation of Emi1 ...optokinetic behavior / regulation of mRNA cis splicing, via spliceosome / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RMTs methylate histone arginines / AUF1 (hnRNP D0) binds and destabilizes mRNA / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / GLI3 is processed to GLI3R by the proteasome / TNFR1-mediated ceramide production / Hedgehog 'on' state / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Negative regulation of MET activity / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Protein methylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Regulation of signaling by CBL / Endosomal Sorting Complex Required For Transport (ESCRT) / Protein hydroxylation / KEAP1-NFE2L2 pathway / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / Deactivation of the beta-catenin transactivating complex / PINK1-PRKN Mediated Mitophagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of RUNX3 expression and activity / mTORC1-mediated signalling / Regulation of FZD by ubiquitination / brain segmentation / p75NTR recruits signalling complexes / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Interleukin-1 signaling / nucleate erythrocyte maturation / ABC-family proteins mediated transport / Regulation of TNFR1 signaling / Antigen processing: Ubiquitination & Proteasome degradation / NOD1/2 Signaling Pathway / convergent extension involved in gastrulation / Ovarian tumor domain proteases / Ub-specific processing proteases / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Neddylation / Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / The role of GTSE1 in G2/M progression after G2 checkpoint / convergent extension involved in axis elongation / primitive hemopoiesis / embryonic retina morphogenesis in camera-type eye / Aggrephagy / hemoglobin biosynthetic process / chordate embryonic development / embryonic brain development
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 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 / 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 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 / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL28 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL28 / 60S ribosomal protein L37a / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S24 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / 60S ribosomal protein L32 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S27 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein eS4 / Ribosomal protein L18 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL33 / 40S ribosomal protein S6 / Ribosomal protein L15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL39 / Ribosomal protein L5b / Large ribosomal subunit protein uL5 / Ribosomal protein L37 / 60S ribosomal protein L21 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein uS4 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Ribosomal protein S14 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L7a / FAU ubiquitin-like and ribosomal protein S30 fusion a / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Ribosomal protein L26 / Ribosomal protein S10 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL16 / DNA-(apurinic or apyrimidinic site) lyase / Ribosomal protein L4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL13
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
Revision 1.4Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary / Category: em_admin / pdbx_entry_details
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

+
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

+
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

-
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

-
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

-
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)

-
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

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 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 %

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more