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- EMDB-14627: Murine Elongator Elp456 subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-14627
TitleMurine Elongator Elp456 subcomplex
Map data
Sample
  • Complex: Elp4, Elp5, Elp6
KeywordstRNA modification / Elp4 / Elp5 / Elp6 / Elongator Elp456 subcomplex / hexameric ring / TRANSLATION
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsGaik M / Glatt S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: EMBO Mol Med / Year: 2022
Title: Functional divergence of the two Elongator subcomplexes during neurodevelopment.
Authors: Monika Gaik / Marija Kojic / Megan R Stegeman / Tülay Öncü-Öner / Anna Kościelniak / Alun Jones / Ahmed Mohamed / Pak Yan Stefanie Chau / Sazia Sharmin / Andrzej Chramiec-Głąbik / ...Authors: Monika Gaik / Marija Kojic / Megan R Stegeman / Tülay Öncü-Öner / Anna Kościelniak / Alun Jones / Ahmed Mohamed / Pak Yan Stefanie Chau / Sazia Sharmin / Andrzej Chramiec-Głąbik / Paulina Indyka / Michał Rawski / Anna Biela / Dominika Dobosz / Amanda Millar / Vann Chau / Aycan Ünalp / Michael Piper / Mark C Bellingham / Evan E Eichler / Deborah A Nickerson / Handan Güleryüz / Nour El Hana Abbassi / Konrad Jazgar / Melissa J Davis / Saadet Mercimek-Andrews / Sultan Cingöz / Brandon J Wainwright / Sebastian Glatt /
Abstract: The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have ...The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient-derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.
History
DepositionMar 26, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14627.png

Downloads & links

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Map

FileDownload / File: emd_14627.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.21515763 - 0.45549616
Average (Standard dev.)-0.002028751 (±0.01950686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14627_msk_1.map
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Half map: #2

Fileemd_14627_half_map_1.map
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Half map: #1

Fileemd_14627_half_map_2.map
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Sample components

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Entire : Elp4, Elp5, Elp6

EntireName: Elp4, Elp5, Elp6
Components
  • Complex: Elp4, Elp5, Elp6

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Supramolecule #1: Elp4, Elp5, Elp6

SupramoleculeName: Elp4, Elp5, Elp6 / type: complex / ID: 1 / Parent: 0 / Details: hexameric ring
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 200 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.58 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 2 mM MgCl2, 5 mM DTT)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 4121 / Average electron dose: 41.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 336000
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 252000
DetailsFrame alignment and dose weighting were performed with MotionCor2 (using Fourier space cropping by a factor of 2, resulting in a pixel size of 1.72), and contrast transfer function was determined with CTFIND4.
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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