[English] 日本語
Yorodumi
- EMDB-14985: EM map of the LARGE1 dual glycosyltransferase without its coiled-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14985
TitleEM map of the LARGE1 dual glycosyltransferase without 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 / 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
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: 3.65 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

-
Structure visualization

Supplemental images

emd_14985.png

Downloads & links

-
Map

FileDownload / File: emd_14985.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered map
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0514
Minimum - Maximum-0.19055969 - 0.31959125
Average (Standard dev.)0.001122749 (±0.010609455)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_14985_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unfiltered map

Fileemd_14985_additional_1.map
AnnotationUnfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_14985_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_14985_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LARGE1

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

-
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

-
Macromolecule #1: LARGE1

MacromoleculeName: LARGE1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GNHSKTYSME EGTGDSENLR AGIVA GNSS ECGQQPVVEK CETIHVAIVC AGYNASRDVV TLVKSVLFHR RNPLHFHLIA DSIAEQ ILA TLFQTWMVPA VRVDFYNADE LKSEVSWIPN KHYSGIYGLM KLVLTKTLPA NLERVIV LD TDITFATDIA ELWAVFHKFK ...String:
GNHSKTYSME EGTGDSENLR AGIVA GNSS ECGQQPVVEK CETIHVAIVC AGYNASRDVV TLVKSVLFHR RNPLHFHLIA DSIAEQ ILA TLFQTWMVPA VRVDFYNADE LKSEVSWIPN KHYSGIYGLM KLVLTKTLPA NLERVIV LD TDITFATDIA ELWAVFHKFK GQQVLGLVEN QSDWYLGNLW KNHRPWPALG RGYNTGVI L LLLDKLRKMK WEQMWRLTAE RELMGMLSTS LADQDIFNAV IKQNPFLVYQ LPCFWNVQL SDHTRSEQCY RDVSDLKVIH WNSPKKLRVK NKHVEFFRNL YLTFLEYDGN LLRRELFGCP SEADVNSEN LQKQLSELDE DDLCYEFRRE RFTVHRTHLY FLHYEYEPAA DSTDVTLVAQ L SMDRLQML EAICKHWEGP ISLALYLSDA EAQQFLRYAQ GSEVLMSRHN VGYHIVYKEG QF YPVNLLR NVAMKHISTP YMFLSDIDFL PMYGLYEYLR KSVIQLDLAN TKKAMIVPAF ETL RYRLSF PKSKAELLSM LDMGTLFTFR YHVWTKGHAP TNFAKWRTAT TPYRVEWEAD FEPY VVVRR DCPEYDRRFV GFGWNKVAHI MELDVQEYEF IVLPNAYMIH MPHAPSFDIT KFRSN KQYR ICLKTLKEEF QQDMSRRYGF AALKYLTAEN NSGSGGHHHH HH

UniProtKB: Xylosyl- and glucuronyltransferase LARGE1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92093
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.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more