9H6K | pdb_00009h6k

Human B4GALNT1 in Complex with UDP-GalNac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 

Starting Model: in silico
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Literature

Conformational dynamics and membrane insertion mechanism of B4GALNT1 in ganglioside synthesis.

Welland, J.W.J.Barrow, H.G.Stansfeld, P.J.Deane, J.E.

(2025) Nat Commun 16: 5442-5442

  • DOI: https://doi.org/10.1038/s41467-025-60593-9
  • Primary Citation of Related Structures:  
    9H6J, 9H6K, 9H6L

  • PubMed Abstract: 

    Glycosphingolipids (GSLs) are crucial membrane components involved in essential cellular pathways. Complex GSLs, known as gangliosides, are synthesised by glycosyltransferase enzymes and imbalances in GSL metabolism cause severe neurological diseases. B4GALNT1 synthesises the precursors to the major brain gangliosides. Loss of B4GALNT1 function causes hereditary spastic paraplegia, while its overexpression is linked to cancers including childhood neuroblastoma. Here, we present crystal structures of the human homodimeric B4GALNT1 enzyme demonstrating dynamic remodelling of the substrate binding site during catalysis. We show that processing of lipid substrates by B4GALNT1 is severely compromised when surface loops flanking the active site are mutated from hydrophobic residues to polar. Molecular dynamics simulations support that these loops can insert into the lipid bilayer explaining how B4GALNT1 accesses and processes lipid substrates. By combining structure prediction and molecular simulations we propose that this mechanism of dynamic membrane insertion is exploited by other, structurally distinct GSL synthesising enzymes.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-1,4 N-acetylgalactosaminyltransferase 1
A, B
499Homo sapiensMutation(s): 0 
Gene Names: B4GALNT1GALGTSIAT2
EC: 2.4.1.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q00973 (Homo sapiens)
Explore Q00973 
Go to UniProtKB:  Q00973
PHAROS:  Q00973
GTEx:  ENSG00000135454 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00973
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q00973-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UD2 (Subject of Investigation/LOI)
Query on UD2

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-NESSUJCYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.1α = 90
b = 134.922β = 95.907
c = 86.584γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata collection
Aimlessdata scaling
PHASERphasing
ISOLDEmodel building
Cootmodel building
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release