5M2M image
Deposition Date 2016-10-13
Release Date 2017-08-30
Last Version Date 2024-11-20
Entry Detail
PDB ID:
5M2M
Keywords:
Title:
Complex between human TNF alpha and Llama VHH3
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Lama glama (Taxon ID: 9844)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Tumor necrosis factor
Gene (Uniprot):TNF
Chain IDs:A, B, C, G, I, K (auth: M)
Chain Length:157
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Llama nanobody VHH3
Chain IDs:D, E, F, H, J, L (auth: N)
Chain Length:129
Number of Molecules:6
Biological Source:Lama glama
Primary Citation
Bivalent Llama Single-Domain Antibody Fragments against Tumor Necrosis Factor Have Picomolar Potencies due to Intramolecular Interactions.
Front Immunol 8 867 867 (2017)
PMID: 28824615 DOI: 10.3389/fimmu.2017.00867

Abstact

The activity of tumor necrosis factor (TNF), a cytokine involved in inflammatory pathologies, can be inhibited by antibodies or trap molecules. Herein, llama-derived variable heavy-chain domains of heavy-chain antibody (VHH, also called Nanobodies™) were generated for the engineering of bivalent constructs, which antagonize the binding of TNF to its receptors with picomolar potencies. Three monomeric VHHs (VHH#1, VHH#2, and VHH#3) were characterized in detail and found to bind TNF with sub-nanomolar affinities. The crystal structures of the TNF-VHH complexes demonstrate that VHH#1 and VHH#2 share the same epitope, at the center of the interaction area of TNF with its TNFRs, while VHH#3 binds to a different, but partially overlapping epitope. These structures rationalize our results obtained with bivalent constructs in which two VHHs were coupled via linkers of different lengths. Contrary to conventional antibodies, these bivalent Nanobody™ constructs can bind to a single trimeric TNF, thus binding with avidity and blocking two of the three receptor binding sites in the cytokine. The different mode of binding to antigen and the engineering into bivalent constructs supports the design of highly potent VHH-based therapeutic entities.

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Primary Citation of related structures