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- EMDB-13114: Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b -
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Open data
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Basic information
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Title | Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b | ||||||||||||||||||
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![]() | translation / embryo / zebrafish / maternal / Dap1 / Dap1b / Habp4 / Eif5a / Eef2b / ribosome | ||||||||||||||||||
Function / homology | ![]() death domain binding / positive regulation of translational termination / ribosome hibernation / PML body organization / positive regulation of translational elongation / SUMO binding / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator ...death domain binding / positive regulation of translational termination / ribosome hibernation / PML body organization / positive regulation of translational elongation / SUMO binding / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / 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 / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / mRNA transport / T cell proliferation involved in immune response / protein-RNA complex assembly / translation elongation factor activity / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / nuclear pore / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / translation repressor activity / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to amino acid starvation / rescue of stalled ribosome / negative regulation of autophagy / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / mRNA 3'-UTR binding / positive regulation of translation / apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / spindle / cytoplasmic ribonucleoprotein granule / rhythmic process / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / virus receptor activity / protein transport / ribosome binding / retina development in camera-type eye / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / protein stabilization / rRNA binding / mitochondrial inner membrane / ribosome / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | ||||||||||||||||||
![]() | Leesch F / Lorenzo-Orts L | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 | ![]() | 391.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 105.1 KB 105.1 KB | Display Display | ![]() |
Images | ![]() | 213.7 KB | ||
Filedesc metadata | ![]() | 22.8 KB | ||
Others | ![]() | 396.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oydMC ![]() 7oyaC ![]() 7oybC ![]() 7oycC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
-Additional map: #1
File | emd_13114_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
+Supramolecule #1: Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
+Macromolecule #1: Ribosomal protein uL1
+Macromolecule #5: 60S ribosomal protein L8
+Macromolecule #6: 40S ribosomal protein SA
+Macromolecule #7: 40S ribosomal protein S26-like
+Macromolecule #8: Ribosomal protein L3
+Macromolecule #9: 40S ribosomal protein S3a
+Macromolecule #10: 40S ribosomal protein S27
+Macromolecule #11: 60S ribosomal protein L4
+Macromolecule #12: 40S ribosomal protein S2
+Macromolecule #13: 40S ribosomal protein S28
+Macromolecule #14: 60S ribosomal protein L5
+Macromolecule #15: Ribosomal protein S3
+Macromolecule #16: 40S ribosomal protein S29
+Macromolecule #17: 60S ribosomal protein L6
+Macromolecule #18: 40S ribosomal protein S4
+Macromolecule #19: 40S ribosomal protein S30
+Macromolecule #20: 60S ribosomal protein L7
+Macromolecule #21: Ribosomal protein S5
+Macromolecule #22: 60S ribosomal protein L7a
+Macromolecule #23: 40S ribosomal protein S6
+Macromolecule #24: RACK1
+Macromolecule #25: 60S ribosomal protein L9
+Macromolecule #26: 40S ribosomal protein S7
+Macromolecule #27: 60S ribosomal protein L10
+Macromolecule #28: 40S ribosomal protein S8
+Macromolecule #29: 60S ribosomal protein L11
+Macromolecule #30: 40S ribosomal protein S9
+Macromolecule #32: S10_plectin domain-containing protein
+Macromolecule #33: 60S ribosomal protein L13
+Macromolecule #34: 40S ribosomal protein S11
+Macromolecule #35: 60S ribosomal protein L14
+Macromolecule #36: Ribosomal protein L15
+Macromolecule #37: 40S ribosomal protein S13
+Macromolecule #38: 60S ribosomal protein L13a
+Macromolecule #39: 40S ribosomal protein S14-like
+Macromolecule #40: 60S ribosomal protein L17
+Macromolecule #41: 40S ribosomal protein uS19
+Macromolecule #42: Ribosomal protein L18
+Macromolecule #43: Ribosomal protein S16
+Macromolecule #44: Ribosomal protein L19
+Macromolecule #45: 40S ribosomal protein eS17
+Macromolecule #46: 60S ribosomal protein L18a
+Macromolecule #47: 40S ribosomal protein uS13
+Macromolecule #48: 60S ribosomal protein L21
+Macromolecule #49: 40S ribosomal protein S19
+Macromolecule #50: 60S ribosomal protein L22-like
+Macromolecule #51: 40S ribosomal protein uS10
+Macromolecule #52: Ribosomal protein L23
+Macromolecule #53: 40S ribosomal protein S21
+Macromolecule #54: Ribosomal protein L24
+Macromolecule #55: Ribosomal protein S15a
+Macromolecule #56: 60S ribosomal protein L23a
+Macromolecule #57: 40S ribosomal protein S23
+Macromolecule #58: Ribosomal protein L26
+Macromolecule #59: 40S ribosomal protein S24
+Macromolecule #60: 60S ribosomal protein L27
+Macromolecule #61: 40S ribosomal protein S25
+Macromolecule #62: 60S ribosomal protein L27a
+Macromolecule #63: 60S ribosomal protein L29
+Macromolecule #64: 60S ribosomal protein L30
+Macromolecule #65: 60S ribosomal protein L31
+Macromolecule #66: 60S ribosomal protein L32
+Macromolecule #67: 60S ribosomal protein L35a
+Macromolecule #68: 60S ribosomal protein L34
+Macromolecule #69: 60S ribosomal protein L35
+Macromolecule #70: 60S ribosomal protein L36
+Macromolecule #71: Ribosomal protein L37
+Macromolecule #72: 60S ribosomal protein L38
+Macromolecule #73: 60S ribosomal protein L39-like
+Macromolecule #74: Ubiquitin-60S ribosomal protein L40
+Macromolecule #75: 60s ribosomal protein l41
+Macromolecule #76: 60S ribosomal protein L36a-like
+Macromolecule #77: 60S ribosomal protein L37a
+Macromolecule #78: 60S ribosomal protein L28
+Macromolecule #79: 60S ribosomal protein L10E
+Macromolecule #80: Dap1b
+Macromolecule #81: Eukaryotic translation initiation factor 5A-1
+Macromolecule #82: Elongation factor 2
+Macromolecule #83: SERPINE1 mRNA binding protein 1
+Macromolecule #2: 28S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #4: 18S rRNA
+Macromolecule #31: 5S rRNA
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9127 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |