8XX0 | pdb_00008xx0

Crystal structure of anti-IgE antibody HMK-12 Fab complexed with IgE F(ab')2

PDB DOI: https://doi.org/10.2210/pdb8XX0/pdb

Classification: IMMUNE SYSTEM
Organism(s): Rattus norvegicus, Mus musculus
Mutation(s): No

Deposited: 2024-01-17 Released: 2024-07-31
Deposition Author(s): Hirano, T., Koyanagi, A., Kasai, M., Okumura, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.267 (Depositor), 0.270 (DCC)
R-Value Work:
0.225 (Depositor), 0.230 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Allosteric inhibition of IgE-Fc epsilon RI interactions by simultaneous targeting of IgE F(ab')2 epitopes.

Hirano, T., Koyanagi, A., Ago, H., Yamamoto, M., Kitaura, J., Kasai, M., Okumura, K.

(2024) Commun Biol 7: 1042-1042

PubMed: 39179708 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-024-06633-4
Primary Citation of Related Structures:
8XX0

PubMed Abstract:
Immunoglobulin E (IgE) plays pivotal roles in allergic diseases through interaction with a high-affinity receptor (FcεRI). We established that Fab fragments of anti-IgE antibodies (HMK-12 Fab) rapidly dissociate preformed IgE-FcεRI complexes in a temperature-dependent manner and inhibit IgE-mediated anaphylactic reactions, even after allergen challenge. X-ray crystallographic studies revealed that HMK-12 Fab interacts with each of two equivalent epitopes on the Cε2 homodimer domain involved in IgE F(ab')2. Consequently, HMK-12 Fab-mediated targeting of Cε2 reduced the binding affinity of Fc domains and resulted in rapid removal of IgE from the receptor complex. This unexpected finding of allosteric inhibition of IgE-FcεRI interactions by simultaneous targeting of two epitope sites on the Cε2 homodimer domain of IgE F(ab')2 may have implications for the development of novel therapies for allergic disease.

Organizational Affiliation

Department of Hematology, Juntendo University Nerima Hospital, Nerima-ku, Tokyo, Japan. thirano@juntendo.ac.jp.

Macromolecule Content

Total Structure Weight: 108.24 kDa
Atom Count: 7,558
Modelled Residue Count: 957
Deposited Residue Count: 975
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-IgE antibody HMK-12 Fab light chain	A [auth L]	214	Rattus norvegicus	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-IgE antibody HMK-12 Fab heavy chain	B [auth H]	225	Rattus norvegicus	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SPE7 immunoglobulin E F(ab')2 heavy chain	C [auth A]	321	Mus musculus	Mutation(s): 0
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Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth A]
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SPE7 immunoglobulin E F(ab')2 light chain	D [auth B]	215	Mus musculus	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H] mmCIF format, chain M [auth H]	M [auth H]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain H [auth L] SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain G [auth L] MOL2 format, chain F [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain G [auth L] mmCIF format, chain F [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain G [auth L]	F [auth L] G [auth L] H [auth L] I [auth H] J [auth H] F [auth L], G [auth L], H [auth L], I [auth H], J [auth H], K [auth H], L [auth H], N [auth A], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain N [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain N [auth A] Focus chain O [auth B]