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- EMDB-14987: EM map of the LARGE1 dual glycosyltransferase with its coiled-coi... -

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Basic information

Entry
Database: EMDB / ID: EMD-14987
TitleEM map of the LARGE1 dual glycosyltransferase with its coiled-coil stem region
Map dataLocal filtered map
Sample
  • Organelle or cellular component: LARGE1
    • Protein or peptide: LARGE1
Keywordsmatriglycan / xylose / glucuronic acid / polymerase / TRANSFERASE
Function / homology
Function and homology information


post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / walking behavior / Transferases; Glycosyltransferases / striated muscle cell development / connective tissue development / principal sensory nucleus of trigeminal nerve development / skeletal muscle organ development / glycosphingolipid biosynthetic process ...post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / walking behavior / Transferases; Glycosyltransferases / striated muscle cell development / connective tissue development / principal sensory nucleus of trigeminal nerve development / skeletal muscle organ development / glycosphingolipid biosynthetic process / O-linked glycosylation / glucuronosyltransferase activity / UDP-xylosyltransferase activity / localization of cell / protein O-linked mannosylation / reactive gliosis / glycoprotein biosynthetic process / N-acetylglucosamine metabolic process / neuromuscular process controlling posture / retina layer formation / acetylglucosaminyltransferase activity / water transport / retina vasculature development in camera-type eye / plasma membrane organization / basement membrane organization / neuromuscular synaptic transmission / skeletal muscle fiber differentiation / nerve development / skeletal muscle tissue regeneration / hexosyltransferase activity / dentate gyrus development / protein O-linked glycosylation / astrocyte differentiation / synaptic assembly at neuromuscular junction / cardiac muscle cell development / protein targeting to membrane / acetylcholine receptor signaling pathway / Transferases; Glycosyltransferases; Hexosyltransferases / muscle cell cellular homeostasis / blood vessel development / glycosyltransferase activity / protein glycosylation / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / behavioral fear response / response to light stimulus / response to mechanical stimulus / skeletal muscle fiber development / striated muscle contraction / cytoskeleton organization / potassium ion transmembrane transport / myelination / post-translational protein modification / determination of adult lifespan / protein localization to plasma membrane / long-term synaptic potentiation / intracellular protein transport / sensory perception of sound / neuron migration / bone development / neuromuscular junction / multicellular organism growth / memory / manganese ion binding / gene expression / protein-containing complex assembly / Golgi membrane / Golgi apparatus / protein-containing complex / plasma membrane
Similarity search - Function
: / Glycosyl-transferase for dystroglycan / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Xylosyl- and glucuronyltransferase LARGE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsDiskin R / Katz M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS One / Year: 2022
Title: Structural basis for matriglycan synthesis by the LARGE1 dual glycosyltransferase.
Authors: Michael Katz / Ron Diskin /
Abstract: LARGE1 is a bifunctional glycosyltransferase responsible for generating a long linear polysaccharide termed matriglycan that links the cytoskeleton and the extracellular matrix and is required for ...LARGE1 is a bifunctional glycosyltransferase responsible for generating a long linear polysaccharide termed matriglycan that links the cytoskeleton and the extracellular matrix and is required for proper muscle function. This matriglycan polymer is made with an alternating pattern of xylose and glucuronic acid monomers. Mutations in the LARGE1 gene have been shown to cause life-threatening dystroglycanopathies through the inhibition of matriglycan synthesis. Despite its major role in muscle maintenance, the structure of the LARGE1 enzyme and how it assembles in the Golgi are unknown. Here we present the structure of LARGE1, obtained by a combination of X-ray crystallography and single-particle cryo-EM. We found that LARGE1 homo-dimerizes in a configuration that is dictated by its coiled-coil stem domain. The structure shows that this enzyme has two canonical GT-A folds within each of its catalytic domains. In the context of its dimeric structure, the two types of catalytic domains are brought into close proximity from opposing monomers to allow efficient shuttling of the substrates between the two domains. Together, with putative retention of matriglycan by electrostatic interactions, this dimeric organization offers a possible mechanism for the ability of LARGE1 to synthesize long matriglycan chains. The structural information further reveals the mechanisms in which disease-causing mutations disrupt the activity of LARGE1. Collectively, these data shed light on how matriglycan is synthesized alongside the functional significance of glycosyltransferase oligomerization.
History
DepositionMay 17, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_14987.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å
1.04 Å/pix.
x 200 pix.
= 208. Å
1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.153
Minimum - Maximum-0.3539706 - 0.8531006
Average (Standard dev.)0.0040571406 (±0.03540753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14987_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unfiltered map

Fileemd_14987_additional_1.map
AnnotationUnfiltered map
Projections & Slices
AxesZYX

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Half map: Half map B

Fileemd_14987_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Half map: Half map A

Fileemd_14987_half_map_2.map
AnnotationHalf map A
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Sample components

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Entire : LARGE1

EntireName: LARGE1
Components
  • Organelle or cellular component: LARGE1
    • Protein or peptide: LARGE1

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Supramolecule #1: LARGE1

SupramoleculeName: LARGE1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: LARGE1

MacromoleculeName: LARGE1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHGSGG LFSGSFEDGK PVSLSPLESQ AHSPRYTASS QR ERESLEV RMREVEEENR ALRRQLSLAQ GRAPSHRRGN HSKTYSMEEG TGDSENLRAG IVA GNSSEC GQQPVVEKCE TIHVAIVCAG YNASRDVVTL VKSVLFHRRN PLHFHLIADS IAEQ ILATL ...String:
HHHHHHGSGG LFSGSFEDGK PVSLSPLESQ AHSPRYTASS QR ERESLEV RMREVEEENR ALRRQLSLAQ GRAPSHRRGN HSKTYSMEEG TGDSENLRAG IVA GNSSEC GQQPVVEKCE TIHVAIVCAG YNASRDVVTL VKSVLFHRRN PLHFHLIADS IAEQ ILATL FQTWMVPAVR VDFYNADELK SEVSWIPNKH YSGIYGLMKL VLTKTLPANL ERVIV LDTD ITFATDIAEL WAVFHKFKGQ QVLGLVENQS DWYLGNLWKN HRPWPALGRG YNTGVI LLL LDKLRKMKWE QMWRLTAERE LMGMLSTSLA DQDIFNAVIK QNPFLVYQLP CFWNVQL SD HTRSEQCYRD VSDLKVIHWN SPKKLRVKNK HVEFFRNLYL TFLEYDGNLL RRELFGCP S EADVNSENLQ KQLSELDEDD LCYEFRRERF TVHRTHLYFL HYEYEPAADS TDVTLVAQL SMDRLQMLEA ICKHWEGPIS LALYLSDAEA QQFLRYAQGS EVLMSRHNVG YHIVYKEGQF YPVNLLRNV AMKHISTPYM FLSDIDFLPM YGLYEYLRKS VIQLDLANTK KAMIVPAFET L RYRLSFPK SKAELLSMLD MGTLFTFRYH VWTKGHAPTN FAKWRTATTP YRVEWEADFE PY VVVRRDC PEYDRRFVGF GWNKVAHIME LDVQEYEFIV LPNAYMIHMP HAPSFDITKF RSN KQYRIC LKTLKEEFQQ DMSRRYGFAA LKYLTAENNS

UniProtKB: Xylosyl- and glucuronyltransferase LARGE1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 77.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164336
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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