8P2E | pdb_00008p2e

Homotypic interacting B1 fab bound to Chondroitin Sulfate A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate.

Vidal-Calvo, E.E.Martin-Salazar, A.Choudhary, S.Dagil, R.Raghavan, S.S.R.Duvnjak, L.Nordmaj, M.A.Clausen, T.M.Skafte, A.Oberkofler, J.Wang, K.Agerbaek, M.O.Loppke, C.Jorgensen, A.M.Ropac, D.Mujollari, J.Willis, S.Garcias Lopez, A.Miller, R.L.Karlsson, R.T.G.Goerdeler, F.Chen, Y.H.Colaco, A.R.Wang, Y.Lavstsen, T.Martowicz, A.Nelepcu, I.Marzban, M.Oo, H.Z.Orum-Madsen, M.S.Wang, Y.Nielsen, M.A.Clausen, H.Wierer, M.Wolf, D.Gogenur, I.Theander, T.G.Al-Nakouzi, N.Gustavsson, T.Daugaard, M.Salanti, A.

(2024) Nat Commun 15: 7553-7553

  • DOI: https://doi.org/10.1038/s41467-024-51781-0
  • Primary Citation of Related Structures:  
    8P2E

  • PubMed Abstract: 

    Molecular similarities between embryonic and malignant cells can be exploited to target tumors through specific signatures absent in healthy adult tissues. One such embryonic signature tumors express is oncofetal chondroitin sulfate (ofCS), which supports disease progression and dissemination in cancer. Here, we report the identification and characterization of phage display-derived antibody fragments recognizing two distinct ofCS epitopes. These antibody fragments show binding affinity to ofCS in the low nanomolar range across a broad selection of solid tumor types in vitro and in vivo with minimal binding to normal, inflamed, or benign tumor tissues. Anti-ofCS antibody drug conjugates and bispecific immune cell engagers based on these targeting moieties disrupt tumor progression in animal models of human and murine cancers. Thus, anti-ofCS antibody fragments hold promise for the development of broadly effective therapeutic and diagnostic applications targeting human malignancies.


  • Organizational Affiliation
    • Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark. elena@sund.ku.dk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B1 fab light
A, C, E, G
223Homo sapiensMutation(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
B1 fab heavy
B, D, F, H
244Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF22OC0076055
Novo Nordisk FoundationDenmarkNNF21OC0068192
The Carlsberg FoundationDenmarkCF20-0045

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection, Structure summary