+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13113 | ||||||||||||||||||
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Title | Cryo-EM structure of the Xenopus egg 80S ribosome | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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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) / African clawed frog (African clawed frog) | ||||||||||||||||||
Method | 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, 5 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13113.map.gz | 340.9 MB | EMDB map data format | |
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Header (meta data) | emd-13113-v30.xml emd-13113.xml | 97.8 KB 97.8 KB | Display Display | EMDB header |
Images | emd_13113.png | 92 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13113 | HTTPS FTP |
-Related structure data
Related structure data | 7oycMC 7oyaC 7oybC 7oydC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13113.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Xenopus egg 80S ribosome
+Supramolecule #1: Xenopus egg 80S ribosome
+Macromolecule #1: Eukaryotic translation initiation factor 5A
+Macromolecule #6: 60S ribosomal protein L8
+Macromolecule #7: 40S ribosomal protein SA
+Macromolecule #8: Rpl3-prov protein
+Macromolecule #9: 40S ribosomal protein S3a-A
+Macromolecule #10: 60S ribosomal protein L4-B
+Macromolecule #11: 40S ribosomal protein S2
+Macromolecule #12: Rpl5-b protein
+Macromolecule #13: DNA-(apurinic or apyrimidinic site) lyase
+Macromolecule #14: 60S ribosomal protein L6
+Macromolecule #15: 40S ribosomal protein S4
+Macromolecule #16: MGC130910 protein
+Macromolecule #17: Ribosomal_S7 domain-containing protein
+Macromolecule #18: 60S ribosomal protein L7a
+Macromolecule #19: 40S ribosomal protein S6
+Macromolecule #20: 60S ribosomal protein L9
+Macromolecule #21: 40S ribosomal protein S7
+Macromolecule #22: Ribosomal_L16 domain-containing protein
+Macromolecule #23: 40S ribosomal protein S8
+Macromolecule #24: 60S ribosomal protein L11
+Macromolecule #25: 40S ribosomal protein S9
+Macromolecule #26: 40S ribosomal protein S10
+Macromolecule #27: 60S ribosomal protein L13
+Macromolecule #28: 40S ribosomal protein S11
+Macromolecule #29: 60S ribosomal protein L14
+Macromolecule #30: Ribosomal protein L15
+Macromolecule #31: 40S ribosomal protein S13
+Macromolecule #32: 60S ribosomal protein L13a
+Macromolecule #33: Rps14
+Macromolecule #34: 60S ribosomal protein L17
+Macromolecule #35: 40S ribosomal protein S15
+Macromolecule #36: Ribosomal_L18e/L15P domain-containing protein
+Macromolecule #37: Rps16 protein
+Macromolecule #38: 60S ribosomal protein L19
+Macromolecule #39: 40S ribosomal protein S17
+Macromolecule #40: 60S ribosomal protein L18a
+Macromolecule #41: 40S ribosomal protein S18
+Macromolecule #42: 60S ribosomal protein L21
+Macromolecule #43: 40S ribosomal protein S19
+Macromolecule #44: 60S ribosomal protein L22
+Macromolecule #45: 40S ribosomal protein S20
+Macromolecule #46: 60S ribosomal protein L23
+Macromolecule #47: 40S ribosomal protein S21
+Macromolecule #48: TRASH domain-containing protein
+Macromolecule #49: 40S ribosomal protein S15a
+Macromolecule #50: Ribosomal_L23eN domain-containing protein
+Macromolecule #51: 40S ribosomal protein S23
+Macromolecule #52: KOW domain-containing protein
+Macromolecule #53: 40S ribosomal protein S24
+Macromolecule #54: 60S ribosomal protein L27
+Macromolecule #55: 40S ribosomal protein S25
+Macromolecule #56: 60S ribosomal protein L27a
+Macromolecule #57: 40S ribosomal protein S26
+Macromolecule #58: 60S ribosomal protein L29
+Macromolecule #59: 40S ribosomal protein S27
+Macromolecule #60: 60S ribosomal protein L30
+Macromolecule #61: 40S ribosomal protein S28
+Macromolecule #62: 60S ribosomal protein L31
+Macromolecule #63: 40S ribosomal protein S29
+Macromolecule #64: Rpl32
+Macromolecule #65: 40S ribosomal protein S30
+Macromolecule #66: 60S ribosomal protein L35a
+Macromolecule #67: 60S ribosomal protein L34
+Macromolecule #68: Gnb2l1-prov protein
+Macromolecule #69: 60S ribosomal protein L35
+Macromolecule #70: 60S ribosomal protein L36
+Macromolecule #71: HABP4_PAI-RBP1 domain-containing protein
+Macromolecule #72: Ribosomal protein L37
+Macromolecule #73: 60S ribosomal protein L38
+Macromolecule #74: MGC116452 protein
+Macromolecule #75: 60S ribosomal protein L40
+Macromolecule #76: Rpl41
+Macromolecule #77: MGC85428 protein
+Macromolecule #78: Rpl37a
+Macromolecule #79: 60S ribosomal protein L28
+Macromolecule #80: Death-associated protein-like 1-B
+Macromolecule #81: Eef2-prov protein
+Macromolecule #2: 18S rRNA
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #82: MAGNESIUM ION
+Macromolecule #83: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14) |
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Final 3D classification | Number classes: 4 / Software - Name: cryoSPARC (ver. 2.14) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.14) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 412340 |