+Open data
-Basic information
Entry | Database: PDB / ID: 7oyd | ||||||||||||||||||
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Title | Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / translation / embryo / zebrafish / maternal / Dap1 / Dap1b / Habp4 / Eif5a / Eef2b | ||||||||||||||||||
Function / homology | Function and homology information death domain binding / non-membrane-bounded organelle / positive regulation of translational termination / ribosome hibernation / translation elongation factor binding / PML body organization / positive regulation of translational elongation / SUMO binding / ribosomal subunit / regulation of G1 to G0 transition ...death domain binding / non-membrane-bounded organelle / positive regulation of translational termination / ribosome hibernation / translation elongation factor binding / PML body organization / positive regulation of translational elongation / SUMO binding / ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / translational elongation / 90S preribosome / TOR signaling / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / translation elongation factor activity / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / rough endoplasmic reticulum / translation repressor activity / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / translation initiation factor binding / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to amino acid starvation / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of autophagy / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / small-subunit processome / mRNA 3'-UTR binding / apoptotic signaling pathway / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / spindle / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosomal small subunit biogenesis / rhythmic process / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / retina development in camera-type eye / ribosomal small subunit assembly / virus receptor activity / ribosomal large subunit assembly / small ribosomal subunit / T cell differentiation in thymus / large ribosomal subunit rRNA binding / cell body / 5S rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / negative regulation of translation / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome Similarity search - Function | ||||||||||||||||||
Biological species | Danio rerio (zebrafish) Oryctolagus cuniculus (rabbit) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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 | 7oyd.cif.gz | 4.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oyd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oyd_validation.pdf.gz | 916.7 KB | Display | wwPDB validaton report |
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Full document | 7oyd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7oyd_validation.xml.gz | 290.5 KB | Display | |
Data in CIF | 7oyd_validation.cif.gz | 476.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oyd ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oyd | HTTPS FTP |
-Related structure data
Related structure data | 13114MC 7oyaC 7oybC 7oycC 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
-Ribosomal protein ... , 13 types, 13 molecules xBDDFFNQQQRVWWWYj
#1: Protein | Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8 |
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#8: Protein | Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06 |
#15: Protein | Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3 |
#21: Protein | Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5 |
#36: Protein | Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1 |
#42: Protein | Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#43: Protein | Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4 |
#44: Protein | Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TYL6 |
#52: Protein | Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1 |
#54: Protein | Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28 |
#55: Protein | Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89 |
#58: Protein | Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0 |
#71: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5 |
-RNA chain , 4 types, 4 molecules 589K
#2: RNA chain | Mass: 1213395.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#3: RNA chain | Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_3 |
#4: RNA chain | Mass: 576826.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#31: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4 |
+60S ribosomal protein ... , 34 types, 34 molecules ACDEFGHIJLMOPSTUXZabcdefghikln...
+40S ribosomal protein ... , 25 types, 25 molecules AAAaBBBbCCCcDdEEEeGGHHIIJJLLNNOOPPRRSSTTUUVVXXYYZZ
-Protein , 7 types, 7 molecules GgKKms1tvw
#24: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4 |
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#32: Protein | Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3 |
#74: Protein | Mass: 14771.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#80: Protein | Mass: 12128.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: dap1b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I9N0 |
#81: Protein | Mass: 16954.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P10160 |
#82: Protein | Mass: 95605.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#83: Protein | Mass: 44880.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SW77 |
-Non-polymers , 2 types, 208 molecules
#84: Chemical | ChemComp-MG / #85: Chemical | ChemComp-ZN / |
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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: Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) | ||||||||||||||||||||||||||||||
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 | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9127 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1808120 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 479754 / Details: Composite map of separately refined subunits / Symmetry type: POINT |