6UG8 | pdb_00006ug8

Complex of ch28/11 Fab and SSEA-4 (monoclinic form)

• PDB DOI: https://doi.org/10.2210/pdb6UG8/pdb

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


• Deposited: 2019-09-26 Released: 2019-12-18 
• Deposition Author(s): Soliman, C., Ramsland, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody.

Soliman, C., Chua, J.X., Vankemmelbeke, M., McIntosh, R.S., Guy, A.J., Spendlove, I., Durrant, L.G., Ramsland, P.A.

(2020) J Biological Chem 295: 1009-1020

• PubMed: 31831622 
• DOI: https://doi.org/10.1074/jbc.RA119.011518
• Primary Citation Related Structures: 
  6UG7, 6UG8, 6UG9, 6UGA


• PubMed Abstract: 
  

  Cancer remains a leading cause of morbidity and mortality worldwide, requiring ongoing development of targeted therapeutics such as monoclonal antibodies. Carbohydrates on embryonic cells are often highly expressed in cancer and are therefore attractive targets for antibodies. Stage-specific embryonic antigen-4 (SSEA-4) is one such glycolipid target expressed in many cancers, including breast and ovarian carcinomas. Here, we defined the structural basis for recognition of SSEA-4 by a novel monospecific chimeric antibody (ch28/11). Five X-ray structures of ch28/11 Fab complexes with the SSEA-4 glycan headgroup, determined at 1.5-2.7 Å resolutions, displayed highly similar three-dimensional structures indicating a stable binding mode. The structures also revealed that by adopting a horseshoe-shaped conformation in a deep groove, the glycan headgroup likely sits flat against the membrane to allow the antibody to interact with SSEA-4 on cancer cells. Moreover, we found that the terminal sialic acid of SSEA-4 plays a dominant role in dictating the exquisite specificity of the ch28/11 antibody. This observation was further supported by molecular dynamics simulations of the ch28/11-glycan complex, which show that SSEA-4 is stabilized by its terminal sialic acid, unlike SSEA-3, which lacks this sialic acid modification. These high-resolution views of how a glycolipid interacts with an antibody may help to advance a new class of cancer-targeting immunotherapy.

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Organizational Affiliation: 
• School of Science, RMIT University, Melbourne, Victoria 3083, Australia.
Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom.
Scancell Ltd., Academic Department of Clinical Oncology, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom.
School of Science, RMIT University, Melbourne, Victoria 3083, Australia [e-mail].
Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia.
Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 47.34 kDa 
• Atom Count: 3,605 
• Modeled Residue Count: 425 
• Deposited Residue Count: 431 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ch28/11 Fab light chain	A [auth L]	213	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ch28/11 Fab heavy chain	B [auth H]	218	Mus musculus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C [auth A]	6		N/A
Glycosylation Resources
GlyTouCan: G32254QI GlyCosmos: G32254QI GlyGen: G32254QI

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.464	α = 90
b = 69.167	β = 94.46
c = 97.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Soliman, C., Ramsland, P.A.

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary