9DJW | pdb_00009djw

X-ray crystal structure of TNFa-VNAR D1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 
    0.288 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The structural basis for the selective antagonism of soluble TNF-alpha by shark variable new antigen receptors.

Ubah, O.C.Lake, E.W.Ott, K.L.Priyanka, S.Celeda, S.West, J.L.Gunaratne, G.S.Shi, K.Moeller, N.H.Porter, A.J.Aihara, H.Kosoff, D.LeBeau, A.M.Barelle, C.J.

(2025) Nat Commun 17: 256-256

  • DOI: https://doi.org/10.1038/s41467-025-66967-3
  • Primary Citation Related Structures: 
    9DJW

  • PubMed Abstract: 

    The pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-α) is synthesized as transmembrane TNF-α (tmTNF-α) where proteolytic processing releases soluble TNF-α (sTNF-α). tmTNF-α can act as either a ligand by activating TNF receptors, or a receptor that transmits reverse (outside-to-inside) signalling after binding to native receptors. All TNF-α therapies bind tmTNF-α and induce reverse signalling which can result in immunosuppression leading to infection. We present crystal structures of two anti-TNF-α Variable New Antigen Receptors (VNARs) in complex with sTNF-α via two distinct epitopes. The VNAR-D1 recognizes an epitope that selectively engages sTNF-α while VNAR-C4 binds an epitope that partially overlaps with other biologic therapies. In activated CD4 + T cells, our VNARs do not induce reverse signalling in contrast to currently available therapies. Our findings suggest that neutralization through a unique mechanism may lead to anti-TNF-α agents with an improved safety profile that will benefit high-risk patients.


  • Organizational Affiliation
    • Elasmogen Ltd., Aberdeen, UK. obinna.ubah@elasmogen.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen receptor129Squalus acanthiasMutation(s): 0 
Gene Names: NAR
UniProt
Find proteins for Q8JGJ1 (Ginglymostoma cirratum)
Explore Q8JGJ1 
Go to UniProtKB:  Q8JGJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JGJ1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor156Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
NB [auth P],
WB [auth h],
ZB [auth t]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AC [auth t]
BC [auth t]
CC [auth z]
IB [auth 0]
JB [auth 1]
AC [auth t],
BC [auth t],
CC [auth z],
IB [auth 0],
JB [auth 1],
KB [auth 5],
LB [auth D],
MB [auth J],
OB [auth P],
QB [auth V],
RB [auth W],
SB [auth b],
TB [auth b],
UB [auth b],
VB [auth c],
XB [auth h],
YB [auth n]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
PB [auth S]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free:  0.288 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.32α = 90
b = 218.127β = 96.28
c = 236.485γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 2.0: 2025-10-15
    Type: Coordinate replacement
    Reason: Real space R-factor
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2026-03-25
    Changes: Database references