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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11562 | ||||||||||||
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Title | Mouse Hoxa9 IRES like element bound to the human 80S ribosome | ||||||||||||
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Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||
![]() | Boehringer D / Lenarcic T / Quade N / Leppek K / Fujii K / Susanto TT / Xue S / Genuth NR / Barna M / Ban N | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments. Authors: Kathrin Leppek / Kotaro Fujii / Nick Quade / Teodorus Theo Susanto / Daniel Boehringer / Tea Lenarčič / Shifeng Xue / Naomi R Genuth / Nenad Ban / Maria Barna / ![]() ![]() Abstract: Ribosomes have been suggested to directly control gene regulation, but regulatory roles for ribosomal RNA (rRNA) remain largely unexplored. Expansion segments (ESs) consist of multitudes of tentacle- ...Ribosomes have been suggested to directly control gene regulation, but regulatory roles for ribosomal RNA (rRNA) remain largely unexplored. Expansion segments (ESs) consist of multitudes of tentacle-like rRNA structures extending from the core ribosome in eukaryotes. ESs are remarkably variable in sequence and size across eukaryotic evolution with largely unknown functions. In characterizing ribosome binding to a regulatory element within a Homeobox (Hox) 5' UTR, we identify a modular stem-loop within this element that binds to a single ES, ES9S. Engineering chimeric, "humanized" yeast ribosomes for ES9S reveals that an evolutionary change in the sequence of ES9S endows species-specific binding of Hoxa9 mRNA to the ribosome. Genome editing to site-specifically disrupt the Hoxa9-ES9S interaction demonstrates the functional importance for such selective mRNA-rRNA binding in translation control. Together, these studies unravel unexpected gene regulation directly mediated by rRNA and how ribosome evolution drives translation of critical developmental regulators. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 19.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.1 KB 15.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 165.2 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() | 98.2 MB 98.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 480.1 KB | Display | ![]() |
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Full document | ![]() | 479.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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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: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11562_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11562_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : human 80S ribosome - mouse Hoxa9 IRES like element complex
Entire | Name: human 80S ribosome - mouse Hoxa9 IRES like element complex |
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Components |
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-Supramolecule #1: human 80S ribosome - mouse Hoxa9 IRES like element complex
Supramolecule | Name: human 80S ribosome - mouse Hoxa9 IRES like element complex type: complex / ID: 1 / Parent: 0 / Details: Hoxa9 IRES was produced by in vitro transcription |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: 80S ribosome
Supramolecule | Name: 80S ribosome / type: organelle_or_cellular_component / ID: 2 / Parent: 1 |
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-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 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |