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- PDB-8p2e: Homotypic interacting B1 fab bound to Chondroitin Sulfate A -

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Basic information

Entry
Database: PDB / ID: 8p2e
TitleHomotypic interacting B1 fab bound to Chondroitin Sulfate A
Components
  • B1 fab heavy
  • B1 fab light
KeywordsSUGAR BINDING PROTEIN / Chondroitin Sulfate A
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRaghavan, S.S.R. / Dagil, R. / Wang, K.T. / Salanti, A.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF22OC0076055 Denmark
Novo Nordisk FoundationNNF21OC0068192 Denmark
The Carlsberg FoundationCF20-0045 Denmark
CitationJournal: Nat Commun / Year: 2024
Title: Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate.
Authors: Elena Ethel Vidal-Calvo / Anne Martin-Salazar / Swati Choudhary / Robert Dagil / Sai Sundar Rajan Raghavan / Lara Duvnjak / Mie Anemone Nordmaj / Thomas Mandel Clausen / Ann Skafte / Jan ...Authors: Elena Ethel Vidal-Calvo / Anne Martin-Salazar / Swati Choudhary / Robert Dagil / Sai Sundar Rajan Raghavan / Lara Duvnjak / Mie Anemone Nordmaj / Thomas Mandel Clausen / Ann Skafte / Jan Oberkofler / Kaituo Wang / Mette Ø Agerbæk / Caroline Løppke / Amalie Mundt Jørgensen / Daria Ropac / Joana Mujollari / Shona Willis / Agnès Garcias López / Rebecca Louise Miller / Richard Torbjörn Gustav Karlsson / Felix Goerdeler / Yen-Hsi Chen / Ana R Colaço / Yong Wang / Thomas Lavstsen / Agnieszka Martowicz / Irina Nelepcu / Mona Marzban / Htoo Zarni Oo / Maj Sofie Ørum-Madsen / Yuzhuo Wang / Morten A Nielsen / Henrik Clausen / Michael Wierer / Dominik Wolf / Ismail Gögenur / Thor G Theander / Nader Al-Nakouzi / Tobias Gustavsson / Mads Daugaard / Ali Salanti /
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 ...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.
History
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jun 5, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 5, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B1 fab light
B: B1 fab heavy
C: B1 fab light
D: B1 fab heavy
E: B1 fab light
F: B1 fab heavy
G: B1 fab light
H: B1 fab heavy


Theoretical massNumber of molelcules
Total (without water)200,3288
Polymers200,3288
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17230 Å2
ΔGint-93 kcal/mol
Surface area72150 Å2

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Components

#1: Antibody
B1 fab light


Mass: 23662.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
B1 fab heavy


Mass: 26419.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: B1 fabs bound to chondroitin sulphate A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 50 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1250000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213275
ELECTRON MICROSCOPYf_angle_d0.81518048
ELECTRON MICROSCOPYf_dihedral_angle_d13.2594749
ELECTRON MICROSCOPYf_chiral_restr0.0382030
ELECTRON MICROSCOPYf_plane_restr0.0042316

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