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- EMDB-26540: CryoEM structure of LARGE1 from C1 reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-26540
TitleCryoEM structure of LARGE1 from C1 reconstruction
Map data
Sample
  • Complex: LARGE1
    • Protein or peptide: Xylosyl- and glucuronyltransferase LARGE1
  • Ligand: MANGANESE (II) ION
KeywordsGlycosyltransferase / Metalloenzyme / TRANSFERASE
Function / homology
Function and homology information


Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / skeletal muscle organ development / glucuronosyltransferase activity / Matriglycan biosynthesis on DAG1 / Transferases; Glycosyltransferases / UDP-xylosyltransferase activity / protein O-linked glycosylation via mannose / glycosphingolipid biosynthetic process / negative regulation of muscle cell apoptotic process ...Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / skeletal muscle organ development / glucuronosyltransferase activity / Matriglycan biosynthesis on DAG1 / Transferases; Glycosyltransferases / UDP-xylosyltransferase activity / protein O-linked glycosylation via mannose / glycosphingolipid biosynthetic process / negative regulation of muscle cell apoptotic process / positive regulation of skeletal muscle acetylcholine-gated channel clustering / N-acetylglucosamine metabolic process / acetylglucosaminyltransferase activity / hexosyltransferase activity / protein O-linked glycosylation / skeletal muscle tissue regeneration / glycoprotein biosynthetic process / muscle cell cellular homeostasis / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of Rac protein signal transduction / neuromuscular junction / manganese ion binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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: 3.7 Å
AuthorsJoseph S / Schnicker NJ / Campbell KP
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)U54NS053672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: To Be Published
Title: CryoEM structure of LARGE1 from C1 reconstruction
Authors: Campbell KP
History
DepositionMar 28, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26540.png

Downloads & links

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Map

FileDownload / File: emd_26540.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 300 pix.
= 240.45 Å		0.8 Å/pix.
x 300 pix.
= 240.45 Å		0.8 Å/pix.
x 300 pix.
= 240.45 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8015 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.0016936355 - 2.5425768
Average (Standard dev.)0.0015777564 (±0.028812371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 240.45001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26540_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26540_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LARGE1

EntireName: LARGE1
Components
  • Complex: LARGE1
    • Protein or peptide: Xylosyl- and glucuronyltransferase LARGE1
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: LARGE1

SupramoleculeName: LARGE1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: No transmembrane region
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 211 KDa

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Macromolecule #1: Xylosyl- and glucuronyltransferase LARGE1

MacromoleculeName: Xylosyl- and glucuronyltransferase LARGE1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Transferases; Glycosyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.806242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSALLILALV GAAVADYKDH DGDYKDHDID YKDDDDKLAA AFEDGKPVSL SPLESQAHSP RYTASSQRER ESLEVRMREV EEENRALRR QLSLAQGRAP SHRRGNHSKT YSMEEGTGDS ENLRAGIVAG NSSECGQQPV VEKCETIHVA IVCAGYNASR D VVTLVKSV ...String:
MSALLILALV GAAVADYKDH DGDYKDHDID YKDDDDKLAA AFEDGKPVSL SPLESQAHSP RYTASSQRER ESLEVRMREV EEENRALRR QLSLAQGRAP SHRRGNHSKT YSMEEGTGDS ENLRAGIVAG NSSECGQQPV VEKCETIHVA IVCAGYNASR D VVTLVKSV LFHRRNPLHF HLIADSIAEQ ILATLFQTWM VPAVRVDFYN ADELKSEVSW IPNKHYSGIY GLMKLVLTKT LP ANLERVI VLDTDITFAT DIAELWAVFH KFKGQQVLGL VENQSDWYLG NLWKNHRPWP ALGRGYNTGV ILLLLDKLRK MKW EQMWRL TAERELMGML STSLADQDIF NAVIKQNPFL VYQLPCFWNV QLSDHTRSEQ CYRDVSDLKV IHWNSPKKLR VKNK HVEFF RNLYLTFLEY DGNLLRRELF GCPSEADVNS ENLQKQLSEL DEDDLCYEFR RERFTVHRTH LYFLHYEYEP AADST DVTL VAQLSMDRLQ MLEAICKHWE GPISLALYLS DAEAQQFLRY AQGSEVLMSR HNVGYHIVYK EGQFYPVNLL RNVAMK HIS TPYMFLSDID FLPMYGLYEY LRKSVIQLDL ANTKKAMIVP AFETLRYRLS FPKSKAELLS MLDMGTLFTF RYHVWTK GH APTNFAKWRT ATTPYRVEWE ADFEPYVVVR RDCPEYDRRF VGFGWNKVAH IMELDVQEYE FIVLPNAYMI HMPHAPSF D ITKFRSNKQY RICLKTLKEE FQQDMSRRYG FAALKYLTAE NNSHHHHHH

UniProtKB: Xylosyl- and glucuronyltransferase LARGE1

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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

Concentration0.5 mg/mL
BufferpH: 6.6
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.664 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1742250
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 81263
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

DetailsUsed initial model from Alphafold2
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7ui6:
CryoEM structure of LARGE1 from C1 reconstruction

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