+Open data
-Basic information
Entry | Database: PDB / ID: 7oyb | ||||||||||||||||||
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Title | Cryo-EM structure of the 6 hpf zebrafish embryo 80S ribosome | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / translation / embryo / zebrafish / maternal | ||||||||||||||||||
Function / homology | Function and homology information optokinetic behavior / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / TNFR1-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 ...optokinetic behavior / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / 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 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / convergent extension involved in gastrulation / : / primitive hemopoiesis / embryonic retina morphogenesis in camera-type eye / mitochondrial cytochrome c oxidase assembly / hemoglobin biosynthetic process / chordate embryonic development / embryonic brain development / positive regulation of gastrulation / ribosomal subunit / exocrine pancreas development / anatomical structure development / laminin receptor activity / mitochondrial large ribosomal subunit / positive regulation of translational fidelity / definitive hemopoiesis / pancreas development / regulation of establishment of cell polarity / cytoplasmic side of rough endoplasmic reticulum membrane / erythrocyte development / regulation of innate immune response / negative regulation of Wnt signaling pathway / regulation of cell division / erythrocyte maturation / mitochondrial respiratory chain complex I assembly / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / hemopoiesis / intrinsic apoptotic signaling pathway by p53 class mediator / 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) / hematopoietic stem cell differentiation / vasculogenesis / laminin binding / rough endoplasmic reticulum / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / erythrocyte differentiation / protein kinase C binding / : / brain development / modification-dependent protein catabolic process / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / regulation of erythrocyte differentiation / spindle / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / ribosomal large subunit assembly / regulation of protein localization / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / glucose homeostasis / regulation of translation / T cell differentiation in thymus / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / angiogenesis / mitochondrial inner membrane / negative regulation of translation / rRNA binding / protein ubiquitination / regulation of cell cycle / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / ribonucleoprotein complex Similarity search - Function | ||||||||||||||||||
Biological species | Danio rerio (zebrafish) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 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 | 7oyb.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oyb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oyb ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oyb | HTTPS FTP |
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-Related structure data
Related structure data | 13112MC 7oyaC 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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#2: 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 |
#3: RNA chain | 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 | 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
+40S ribosomal protein ... , 25 types, 25 molecules A2B2C2E2G2H2I2J2L2N2P2R2S2T2U2V2W2X2Y2Z2a2b2c2d2e2
-Ribosomal protein ... , 15 types, 15 molecules B1C1D1F1F2K2N1O2Q1Q2U1X1e1j1l1
#7: Protein | Mass: 46358.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) / References: UniProt: Q5BJJ2 |
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#9: Protein | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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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#51: 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 | 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 | 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 | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Danio rerio (zebrafish) |
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-Non-polymers , 2 types, 210 molecules
#78: Chemical | ChemComp-MG / #79: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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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 6 hpf zebrafish embryosEukaryotic ribosome Type: RIBOSOME / Entity ID: #1-#77 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Danio rerio (zebrafish) / Tissue: 6 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 FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron 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
Software | Name: UCSF ChimeraX / Version: 0.91/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1285670 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 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 building | Protocol: OTHER |