9B74

Crystal structure of humanized 44H10 Fab Version 14

PDB DOI: https://doi.org/10.2210/pdb9B74/pdb

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

Deposited: 2024-03-27 Released: 2024-08-07
Deposition Author(s): Kassardjian, A., Julien, J.P.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.205
R-Value Work: 0.174
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Humanization of Pan-HLA-DR mAb 44H10 Hinges on Critical Residues in the Antibody Framework.

Kassardjian, A., Ivanochko, D., Barber, B., Jetha, A., Julien, J.P.

(2024) Antibodies (Basel) 13

PubMed: 39051333 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/antib13030057
Primary Citation of Related Structures:
9B74, 9B75, 9B76, 9B7B

PubMed Abstract:
Reducing the immunogenicity of animal-derived monoclonal antibodies (mAbs) for use in humans is critical to maximize therapeutic effectiveness and preclude potential adverse events. While traditional humanization methods have primarily focused on grafting antibody Complementarity-Determining Regions (CDRs) on homologous human antibody scaffolds, framework regions can also play essential roles in antigen binding. Here, we describe the humanization of the pan-HLA-DR mAb 44H10, a murine antibody displaying significant involvement of the framework region in antigen binding. Using a structure-guided approach, we identify and restore framework residues that directly interact with the antigen or indirectly modulate antigen binding by shaping the antibody paratope and engineer a humanized antibody with affinity, biophysical profile, and molecular binding basis comparable to that of the parental 44H10 mAb. As a humanized molecule, this antibody holds promise as a scaffold for the development of MHC class II-targeting therapeutics and vaccines.

Organizational Affiliation

Program in Molecular Medicine, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G 0A4, Canada.

Macromolecule Content

Total Structure Weight: 47.74 kDa
Atom Count: 3,563
Modelled Residue Count: 437
Deposited Residue Count: 437
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
h44H10-V14 Antibody, heavy chain	A [auth H]	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
h44H10-V14 Antibody, light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain M [auth L] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain L mmCIF format, chain M [auth L]	C [auth H] D [auth H] E [auth H] F [auth H] J [auth L] C [auth H], D [auth H], E [auth H], F [auth H], J [auth L], K [auth L], L, M [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain P [auth L] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] mmCIF format, chain N [auth L] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L]	N [auth L], O [auth L], P [auth L]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Interactions & Density Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain T [auth L] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L]	G [auth H] H I [auth H] Q [auth L] R [auth L] G [auth H], H, I [auth H], Q [auth L], R [auth L], S [auth L], T [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Interactions & Density Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L]