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- EMDB-11563: Mouse Hoxa9 IRES-like element bound to the human 40S ribosomal su... -

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Basic information

Entry
Database: EMDB / ID: EMD-11563
TitleMouse Hoxa9 IRES-like element bound to the human 40S ribosomal subunit head - IRES binding site
Map datamouse Hoxa9 IRES-like element bound to the human 40S ribosomal subunit
Sample
  • Complex: human 40S ribosomal subunit - mouse Hoxa9 IRES like element complex
    • Organelle or cellular component: 40S ribosomal subunit
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBoehringer D / Lenarcic T / Quade N / Leppek K / Fujii K / Susanto TT / Xue S / Genuth NR / Barna M / Ban N
Funding support United States, Switzerland, 3 items
OrganizationGrant numberCountry
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 Foundation310030B_163478 Switzerland
CitationJournal: 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
DepositionJul 31, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11563.png

Downloads & links

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Map

FileDownload / File: emd_11563.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmouse Hoxa9 IRES-like element bound to the human 40S ribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å		1.39 Å/pix.
x 320 pix.
= 444.8 Å		1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.05843583 - 0.173955
Average (Standard dev.)0.00014888169 (±0.0030432343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0580.1740.000

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Supplemental data

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Mask #1

Fileemd_11563_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_11563_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11563_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : human 40S ribosomal subunit - mouse Hoxa9 IRES like element complex

EntireName: human 40S ribosomal subunit - mouse Hoxa9 IRES like element complex
Components
  • Complex: human 40S ribosomal subunit - mouse Hoxa9 IRES like element complex
    • Organelle or cellular component: 40S ribosomal subunit

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Supramolecule #1: human 40S ribosomal subunit - mouse Hoxa9 IRES like element complex

SupramoleculeName: human 40S ribosomal subunit - mouse Hoxa9 IRES like element complex
type: complex / ID: 1 / Parent: 0
Details: The map includes the binding site of the mouse Hoxa9 IRES-like element bound to the human 40S ribosomal subunit head. (Mouse Hoxa9 IRES was produced by in vitro transcription)
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293-6E cells

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Supramolecule #2: 40S ribosomal subunit

SupramoleculeName: 40S ribosomal subunit / type: organelle_or_cellular_component / ID: 2 / Parent: 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Details: CTF parameters were estimated with with CTFFIND and correction was applied within Relion
Startup modelType of model: NONE
Details: 40S ribosomal subunit 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 ...Details: 40S ribosomal subunit 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: The final map of the IRES binding site on the 40S ribosomal subunit head was obtained after focused classification following a multi-body refinement.
Number images used: 19342
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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