+Open data
-Basic information
Entry | Database: PDB / ID: 7oyc | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Xenopus egg 80S ribosome | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | RIBOSOME / Eif5a / Eef2 / Habp4 / DapL1 / Dap1 / egg / Xenopus | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of translational termination / positive regulation of translational elongation / protein-synthesizing GTPase / laminin receptor activity / mRNA transport / rough endoplasmic reticulum / laminin binding / translation elongation factor activity / nuclear pore / : ...positive regulation of translational termination / positive regulation of translational elongation / protein-synthesizing GTPase / laminin receptor activity / mRNA transport / rough endoplasmic reticulum / laminin binding / translation elongation factor activity / nuclear pore / : / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / spindle / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / protein transport / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / cell division / DNA repair / GTPase activity / apoptotic process / GTP binding / endoplasmic reticulum membrane / RNA binding / zinc ion binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||||||||||||||
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
| ||||||||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7oyc.cif.gz | 4.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7oyc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oyc ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oyc | HTTPS FTP |
---|
-Related structure data
Related structure data | 13113MC 7oyaC 7oybC 7oydC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+Protein , 21 types, 21 molecules 11B1D1D2F1F2I1O2Q1Q2W1X1Y1e1g2i2l1o1p1s1v2
-RNA chain , 4 types, 4 molecules 22517181
#2: RNA chain | 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 | 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 | 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 | 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 |
+60S ribosomal protein ... , 27 types, 27 molecules A1C1E1G1H1J1L1M1O1P1R1S1T1U1V1Z1a1b1c1d1f1g1h1i1k1m1r1
+40S ribosomal protein ... , 26 types, 26 molecules A2B2C2E2G2H2I2J2K2L2N2P2R2S2T2U2V2W2X2Y2Z2a2b2c2d2e2
-Ribosomal protein ... , 2 types, 2 molecules N1j1
#30: Protein | 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 | 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 |
-Protein/peptide , 1 types, 1 molecules n1
#76: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / Tissue: Egg |
---|
-Non-polymers , 2 types, 141 molecules
#82: Chemical | ChemComp-MG / #83: Chemical | ChemComp-ZN / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Xenopus egg 80S ribosome / Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Xenopus laevis (African clawed frog) / Tissue: Egg | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
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 | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 |
-Processing
Software | Name: UCSF ChimeraX / Version: 0.91/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412340 / Symmetry type: POINT |