+Open data
-Basic information
Entry | Database: PDB / ID: 7oya | ||||||||||||||||||
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Title | Cryo-EM structure of the 1 hpf zebrafish embryo 80S ribosome | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / translation / embryo / zebrafish / maternal / Dap1 / Dap1b / Habp4 / Eif5a / Eef2b | ||||||||||||||||||
Function / homology | Function and homology information Hypusine synthesis from eIF5A-lysine / Platelet degranulation / 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 / : / : ...Hypusine synthesis from eIF5A-lysine / Platelet degranulation / 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 / : / Neutrophil degranulation / : / primitive hemopoiesis / embryonic retina morphogenesis in camera-type eye / death domain binding / anatomical structure development / positive regulation of translational termination / ribosome hibernation / hemoglobin biosynthetic process / mitochondrial cytochrome c oxidase assembly / positive regulation of translational elongation / 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 / translational elongation / 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 / mRNA transport / positive regulation of translational initiation / vasculogenesis / erythrocyte development / translation regulator activity / translation elongation factor activity / nuclear pore / 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) / translation repressor activity / translation initiation factor binding / translation initiation factor activity / cellular response to amino acid starvation / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / negative regulation of autophagy / 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 / positive regulation of RNA splicing / 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 / apoptotic signaling pathway / 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 / protein transport / cellular response to xenobiotic stimulus / ribosome binding / glucose homeostasis / regulation of translation Similarity search - Function | ||||||||||||||||||
Biological species | Danio rerio (zebrafish) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||
Authors | Leesch, F. / Lorenzo-Orts, L. / Grishkovskaya, I. / Kandolf, S. / Belacic, K. / Meinhart, A. / Haselbach, D. / Pauli, A. | ||||||||||||||||||
Funding support | Austria, Switzerland, 5items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oya.cif.gz | 4.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oya.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oya_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7oya_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7oya_validation.xml.gz | 301.9 KB | Display | |
Data in CIF | 7oya_validation.cif.gz | 533.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oya ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oya | HTTPS FTP |
-Related structure data
Related structure data | 13111MC 7oybC 7oycC 7oydC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules 22517181
#1: RNA chain | Mass: 625968.500 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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#76: RNA chain | Mass: 1382249.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: GenBank: AL935186.22 |
#77: RNA chain | Mass: 38739.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) |
#78: RNA chain | Mass: 50823.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: GenBank: LR812041.1 |
+40S ribosomal protein ... , 25 types, 25 molecules A2B2C2E2G2H2I2J2L2N2R2V2W2X2Y2a2b2e2P2U2c2d2Z2T2S2
-Ribosomal protein ... , 15 types, 15 molecules O2F2K2Q2e1j1B1C1D1F1N1Q1U1X1l1
#12: Protein | Mass: 16274.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PBW3 |
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#22: Protein | Mass: 22909.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6PC80 |
#23: Protein | Mass: 18919.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7T1J9 |
#25: Protein | Mass: 16387.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q1LWH1 |
#38: Protein | Mass: 15851.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q24JV1 |
#43: Protein | Mass: 11074.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IQJ7 |
#48: Protein | Mass: 46358.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q5BJJ2 |
#49: Protein | Mass: 42644.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7ZW95 |
#50: Protein | Mass: 34118.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IQB1 |
#52: Protein | Mass: 28505.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6Q417 |
#58: Protein | Mass: 24124.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DHS3 |
#61: Protein | Mass: 21045.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6DGL0 |
#64: Protein | Mass: 16316.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: F1QG80 |
#67: Protein | Mass: 17686.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: F1QGI3 |
#69: Protein | Mass: 6410.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6IMW8 |
-Protein , 7 types, 7 molecules D2g2i2p1Y1q1s1
#21: Protein | 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 |
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#29: Protein | Mass: 35161.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: O42248 |
#33: Protein | Mass: 38616.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: B0R085 |
#46: Protein | Mass: 10229.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: A7YY10 |
#68: Protein | Mass: 17387.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q7SXA1 |
#79: Protein | Mass: 43391.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q8AW82 |
#82: Protein | Mass: 12128.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q9I9N0 |
+60S ribosomal protein ... , 29 types, 29 molecules Z1b1c1d1f1g1h1i1k1o1A1E1G1H1J1L1M1O1P1R1T1V1W1n1r1I1S1m1a1
-Eukaryotic translation ... , 2 types, 2 molecules v211
#80: Protein | Mass: 95623.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6P3J5 |
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#81: Protein | Mass: 16987.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q6NX89 |
-Non-polymers , 2 types, 209 molecules
#83: Chemical | ChemComp-ZN / #84: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 80S ribosome from 1 hpf zebrafish embryos / Type: RIBOSOME / Entity ID: #1-#82 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Danio rerio (zebrafish) / Tissue: 1 hpf embryos | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 70 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 43 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1961364 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 535633 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER |