7UT3

Crystal structure of complex of Fab, G10C with GalNAc-pNP

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus
  • Expression System: Sapientia
  • Mutation(s): No 

  • Deposited: 2022-04-26 Released: 2022-09-21 
  • Deposition Author(s): Li, M., Wlodawer, A.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of a GalNAc-Tyrosine-Specific Monoclonal Antibody and Detection of Tyrosine O -GalNAcylation in Numerous Human Tissues and Cell Lines.

Xia, L.Bellomo, T.R.Gibadullin, R.Congdon, M.D.Edmondson, E.F.Li, M.Wlodawer, A.Li, C.Temme, J.S.Patel, P.Butcher, D.Gildersleeve, J.C.

(2022) J Am Chem Soc 144: 16410-16422

  • DOI: https://doi.org/10.1021/jacs.2c04477
  • Primary Citation of Related Structures:  
    7UT3

  • PubMed Abstract: 

    Glycosylation is a vital post-translational modification involved in a range of biological processes including protein folding, signaling, and cell-cell interactions. In 2011, a new type of O -linked glycosylation was discovered, wherein the side-chain oxygen of tyrosine is modified with a GalNAc residue (GalNAc-Tyr). At present, very little is known about GalNAc-Tyr prevalence, function, or biosynthesis. Herein, we describe the design and synthesis of a GalNAc-Tyr-derived hapten and its use in generating a GalNAc-Tyr selective monoclonal antibody. The antibody, G10C, has an unusually high affinity (app K D = 100 pM) and excellent selectivity for GalNAc-Tyr. We also obtained a crystal structure of the G10C Fab region in complex with 4-nitrophenyl- N -acetyl-α-d-galactosaminide (a small molecule mimic of GalNAc-Tyr) providing insights into the structural basis for high affinity and selectivity. Using this antibody, we discovered that GalNAc-Tyr is widely expressed in most human tissues, indicating that it is a ubiquitous and underappreciated post-translational modification. Localization to specific cell types and organ substructures within those tissues indicates that GalNAc-Tyr is likely regulated in a cell-specific manner. GalNAc-Tyr was also observed in a variety of cell lines and primary cells but was only present on the external cell surface in certain cancer cell lines, suggesting that GalNAc-Tyr localization may be altered in cancer cells. Collectively, the results shed new light on this under-studied form of glycosylation and provide access to new tools that will enable expanded biochemical and clinical investigations.


  • Organizational Affiliation

    Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab protein heavy chainA [auth H]217Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G10C Light chainB [auth L]212Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TI0 (Subject of Investigation/LOI)
Query on TI0

Download Ideal Coordinates CCD File 
D [auth L]4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside
C14 H18 N2 O8
OMRLTNCLYHKQCK-RGDJUOJXSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth H]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.594α = 90
b = 132.594β = 90
c = 169.054γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description