9NWU | pdb_00009nwu

Crystal structure of a high affinity VL-VH tetrabody for the erythropoietin receptor

PDB DOI: https://doi.org/10.2210/pdb9NWU/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-03-24 Released: 2025-10-01
Deposition Author(s): Singer, A.U., Bruce, H.A., Yang, N., Blazer, L.L., Adams, J.J., Sidhu, S.S.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

An asymmetric tetrabody is a potent and efficacious agonist of the erythropoietin receptor in vitro and in vivo.

Adams, J.J., Blazer, L.L., Chung, J., Karimi, M., Davidson, T., Bruce, H.A., Singer, A.U., Yang, N., Cardarelli, L., Pot, I., Colombo, L., Huang, L.J., Ma, Y., Michnick, S.W., Moe, O.W., Sidhu, S.S.

(2025) Protein Sci 34: e70292-e70292

PubMed: 40960423 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70292
Primary Citation Related Structures:
9NWU

PubMed Abstract:
Erythropoietin (EPO) initiates EPO receptor (EPOR) signaling in hematopoietic cells by binding to an asymmetric EPOR dimer through two different sites. We engineered dimeric diabody-Fc (Db-Fc) fusion proteins that appeared to act as potent agonists of human EPOR in cell proliferation assays. However, detailed analysis of their oligomeric forms revealed that the predominant Db-Fc species bound EPOR with high affinity but failed to induce cell proliferation. Instead, a minor oligomeric form, identified as a putative tetrabody (Tb) fused to two Fc domains (Tb-Fc ₂), proved to be the minimal active form. The existence of a tetrameric agonist was further supported by crystallography, which revealed an asymmetric Tb structure. Additionally, the structure of an antigen-binding fragment (Fab) bound to EPOR revealed an epitope distinct from the EPO binding sites, and structural modeling showed that engagement of two of the four binding sites on the Tb could form an asymmetric EPOR dimer nearly identical to the active conformation recruited by EPO. In a knock-in mouse model, where mouse EPOR was replaced by human EPOR, purified Tb-Fc ₂ stimulated erythropoiesis with greater potency, efficacy, and duration than darbepoetin, a recombinant EPO that is the leading therapeutic erythropoiesis-stimulating agent (ESA). Collectively, these findings demonstrate that asymmetric tetravalent antibodies such as Tb-Fc ₂ represent promising next-generation ESAs that provide enhanced potency, efficacy, and durability. Moreover, they may reduce the oncogenic and cardiovascular risks associated with the pleiotropy of EPO.

Organizational Affiliation

Anvil Institute for Systems Biologics, Canada.

Macromolecule Content

Total Structure Weight: 99.9 kDa
Atom Count: 7,580
Modeled Residue Count: 903
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diabody	A [auth C], B [auth D], C [auth A], D [auth B]	229	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain G [auth D] SDF format, chain E [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth D] MOL2 format, chain E [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth D] mmCIF format, chain E [auth C]	E [auth C], G [auth D], J [auth A], M [auth B]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain G [auth D] Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth C] Focus chain G [auth D] Focus chain J [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain F [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain F [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain F [auth C]	F [auth C] K [auth A] L [auth A] N [auth B] O [auth B] F [auth C], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain F [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain I [auth D] MOL2 format, chain R [auth B] MOL2 format, chain I [auth D] mmCIF format, chain R [auth B] mmCIF format, chain I [auth D]	I [auth D], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain R [auth B] Interactions & Density Focus chain I [auth D] Focus chain R [auth B]