National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
R01HD086634
United States
European Molecular Biology Organization (EMBO)
ALTF 539-2015
Swiss National Science Foundation
310030B_163478
Switzerland
Citation
Journal: Mol Cell / Year: 2020 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
Deposition
Jul 31, 2020
-
Header (metadata) release
Dec 2, 2020
-
Map release
Dec 2, 2020
-
Update
Dec 30, 2020
-
Current status
Dec 30, 2020
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Entire : Hoxa9 IRES P4 stem-loop bound to the 40S ribosomal subunit
Entire
Name: Hoxa9 IRES P4 stem-loop bound to the 40S ribosomal subunit
Components
Complex: Hoxa9 IRES P4 stem-loop bound to the 40S ribosomal subunit
-
Supramolecule #1: Hoxa9 IRES P4 stem-loop bound to the 40S ribosomal subunit
Supramolecule
Name: Hoxa9 IRES P4 stem-loop bound to the 40S ribosomal subunit type: complex / ID: 1 / Parent: 0 Details: This map contains the 40S ribosomal subunit body, body 1 of a multi-body refinement in Relion. (P4 stem loop RNA was obtained by oligonucleotide synthesis)
Source (natural)
Organism: Homo sapiens (human) / Strain: HEK293-6E cells
Molecular weight
Theoretical: 1.3 MDa
-
Experimental details
-
Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Buffer
pH: 7.6
Grid
Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
Vitrification
Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.5 sec. / Average electron dose: 76.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
+
Image processing
Particle selection
Number selected: 1664622
CTF correction
Software - Name: Gctf
Startup model
Type of model: NONE Details: 40S structure described in Quade, N., Boehringer, D., Leibundgut, M., van den Heuvel, J., and Ban, N., 2015, Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9 A ...Details: 40S structure described in Quade, N., Boehringer, D., Leibundgut, M., van den Heuvel, J., and Ban, N., 2015, Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9 A resolution. Nat. Commun. 6, 7646:1
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION Details: This map contains the 40S ribosomal subunit body, body 1 of a multi-body refinement in Relion. Number images used: 95519
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classification
Software - Name: RELION
FSC plot (resolution estimation)
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi