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Yorodumi- EMDB-14987: EM map of the LARGE1 dual glycosyltransferase with its coiled-coi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14987 | |||||||||
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Title | EM map of the LARGE1 dual glycosyltransferase with its coiled-coil stem region | |||||||||
Map data | Local filtered map | |||||||||
Sample |
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Keywords | matriglycan / xylose / glucuronic acid / polymerase / TRANSFERASE | |||||||||
Function / homology | Function and homology information post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / Transferases; Glycosyltransferases / walking behavior / : / principal sensory nucleus of trigeminal nerve development / striated muscle cell development / connective tissue development / skeletal muscle organ development ...post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / Transferases; Glycosyltransferases / walking behavior / : / principal sensory nucleus of trigeminal nerve development / striated muscle cell development / connective tissue development / skeletal muscle organ development / O-linked glycosylation / localization of cell / glucuronosyltransferase activity / UDP-xylosyltransferase activity / reactive gliosis / glycosphingolipid biosynthetic process / protein O-linked mannosylation / glycoprotein biosynthetic process / N-acetylglucosamine metabolic process / neuromuscular process controlling posture / retina layer formation / water transport / retina vasculature development in camera-type eye / plasma membrane organization / acetylglucosaminyltransferase activity / basement membrane organization / neuromuscular synaptic transmission / skeletal muscle fiber differentiation / skeletal muscle tissue regeneration / nerve development / dentate gyrus development / hexosyltransferase activity / protein O-linked glycosylation / astrocyte differentiation / synaptic assembly at neuromuscular junction / protein targeting to membrane / acetylcholine receptor signaling pathway / cardiac muscle cell development / Transferases; Glycosyltransferases; Hexosyltransferases / muscle cell cellular homeostasis / blood vessel development / glycosyltransferase activity / protein glycosylation / macrophage differentiation / response to light stimulus / Transferases; Glycosyltransferases; Pentosyltransferases / striated muscle contraction / behavioral fear response / skeletal muscle fiber development / response to mechanical stimulus / potassium ion transmembrane transport / cytoskeleton organization / myelination / post-translational protein modification / long-term synaptic potentiation / determination of adult lifespan / protein localization to plasma membrane / sensory perception of sound / intracellular protein transport / neuron migration / multicellular organism growth / neuromuscular junction / bone development / memory / gene expression / manganese ion binding / protein-containing complex assembly / Golgi membrane / Golgi apparatus / protein-containing complex / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.86 Å | |||||||||
Authors | Diskin R / Katz M | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14987.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-14987-v30.xml emd-14987.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14987_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_14987.png | 60.1 KB | ||
Masks | emd_14987_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-14987.cif.gz | 4.9 KB | ||
Others | emd_14987_additional_1.map.gz emd_14987_half_map_1.map.gz emd_14987_half_map_2.map.gz | 14.9 MB 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14987 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14987 | HTTPS FTP |
-Related structure data
Related structure data | 7zvjC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14987.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Local filtered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14987_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered map
File | emd_14987_additional_1.map | ||||||||||||
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Annotation | Unfiltered map | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_14987_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_14987_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : LARGE1
Entire | Name: LARGE1 |
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Components |
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-Supramolecule #1: LARGE1
Supramolecule | Name: LARGE1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: LARGE1
Macromolecule | Name: LARGE1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 77.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |