8P6Q image
Deposition Date 2023-05-28
Release Date 2024-01-24
Last Version Date 2024-10-23
Entry Detail
PDB ID:
8P6Q
Keywords:
Title:
Racemic structure of TNFR1 cysteine-rich domain
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.40 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Tumor necrosis factor-binding protein 1
Gene (Uniprot):TNFRSF1A
Chain IDs:A
Chain Length:45
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(D)
Molecule:D-TNFR-1 CRD2
Chain IDs:B
Chain Length:45
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Deciphering the Synthetic and Refolding Strategy of a Cysteine-Rich Domain in the Tumor Necrosis Factor Receptor (TNF-R) for Racemic Crystallography Analysis and d-Peptide Ligand Discovery.
Acs Bio Med Chem Au 4 68 76 (2024)
PMID: 38404743 DOI: 10.1021/acsbiomedchemau.3c00060

Abstact

Many cell-surface receptors are promising targets for chemical synthesis because of their critical roles in disease development. This synthetic approach enables investigations by racemic protein crystallography and ligand discovery by mirror-image methodologies. However, due to their complex nature, the chemical synthesis of a receptor can be a significant challenge. Here, we describe the chemical synthesis and folding of a central, cysteine-rich domain of the cell-surface receptor tumor necrosis factor 1 which is integral to binding of the cytokine TNF-α, namely, TNFR-1 CRD2. Racemic protein crystallography at 1.4 Å confirmed that the native binding conformation was preserved, and TNFR-1 CRD2 maintained its capacity to bind to TNF-α (KD ≈ 7 nM). Encouraged by this discovery, we carried out mirror-image phage display using the enantiomeric receptor mimic and identified a d-peptide ligand for TNFR-1 CRD2 (KD = 1 μM). This work demonstrated that cysteine-rich domains, including the central domains, can be chemically synthesized and used as mimics for investigations.

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Primary Citation of related structures