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- EMDB-47420: CryoEM structure of LARGE1 bound to UDP -

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Basic information

Entry
Database: EMDB / ID: EMD-47420
TitleCryoEM structure of LARGE1 bound to UDP
Map datalocal sharpened map
Sample
  • Complex: LARGE1
    • Protein or peptide: Xylosyl- and glucuronyltransferase LARGE1
  • Ligand: MANGANESE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE
KeywordsGlycosyltransferase / TRANSFERASE
Function / homology
Function and homology information


post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / principal sensory nucleus of trigeminal nerve development / connective tissue development / Transferases; Glycosyltransferases / walking behavior / glycosphingolipid biosynthetic process / O-linked glycosylation / skeletal muscle organ development ...post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / principal sensory nucleus of trigeminal nerve development / connective tissue development / Transferases; Glycosyltransferases / walking behavior / glycosphingolipid biosynthetic process / O-linked glycosylation / skeletal muscle organ development / glucuronosyltransferase activity / UDP-xylosyltransferase activity / localization of cell / protein O-linked mannosylation / glycoprotein biosynthetic process / N-acetylglucosamine metabolic process / reactive gliosis / neuromuscular process controlling posture / acetylglucosaminyltransferase activity / retina layer formation / water transport / plasma membrane organization / retina vasculature development in camera-type eye / skeletal muscle fiber differentiation / basement membrane organization / nerve development / hexosyltransferase activity / neuromuscular synaptic transmission / dentate gyrus development / skeletal muscle tissue regeneration / 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 / protein glycosylation / blood vessel development / glycosyltransferase activity / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / response to light stimulus / behavioral fear response / striated muscle contraction / response to mechanical stimulus / skeletal muscle fiber development / potassium ion transmembrane transport / cytoskeleton organization / myelination / post-translational protein modification / protein localization to plasma membrane / determination of adult lifespan / intracellular protein transport / sensory perception of sound / neuromuscular junction / bone development / multicellular organism growth / memory / long-term synaptic potentiation / neuron migration / manganese ion binding / protein-containing complex assembly / gene expression / 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: 3.0 Å
AuthorsJoesph S / Spellmon N / 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)U54 NS053672 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)U24 GM129547 United States
CitationJournal: To Be Published
Title: Prodystroglycan defines matriglycan lengths processively polymerized by LARGE1
Authors: Joesph S / Spellmon N / Schnicker NJ / Xu Z / Yang T / Hopkins J / Chakravarthy S / Davulcu O / Anderson ME / Venzke D / Campbell KP
History
DepositionOct 21, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47420.png

Downloads & links

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Map

FileDownload / File: emd_47420.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0078
Minimum - Maximum-0.023530895 - 0.04627809
Average (Standard dev.)0.000007989914 (±0.0012209115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_47420_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_47420_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_47420_half_map_2.map
Annotationhalf map 2
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
  • Ligand: URIDINE-5'-DIPHOSPHATE

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Supramolecule #1: LARGE1

SupramoleculeName: LARGE1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #3: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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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: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 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

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347589
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION (ver. 5)

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