9DJW | pdb_00009djw

X-ray crystal structure of TNFa-VNAR D1 complex

PDB DOI: https://doi.org/10.2210/pdb9DJW/pdb

Classification: TOXIN
Organism(s): Squalus acanthias, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-06 Released: 2025-09-10
Deposition Author(s): Ubah, O.C., Shi, K., Aihara, H., Barelle, C.J., LeBeau, A.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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
View more details

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

PubMed: 41318641 Search on PubMed Search on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 942.44 kDa
Atom Count: 60,848
Modeled Residue Count: 7,845
Deposited Residue Count: 8,550
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen receptor	A [auth 0] B [auth 1] BB [auth t] CB [auth u] DA [auth V] A [auth 0], B [auth 1], BB [auth t], CB [auth u], DA [auth V], DB [auth v], EA [auth W], F [auth 5], FA [auth X], G [auth 6], H [auth 7], HB [auth z], JA [auth b], KA [auth c], L [auth D], LA [auth d], M [auth E], N [auth F], PA [auth h], QA [auth i], R [auth J], RA [auth j], S [auth K], T [auth L], VA [auth n], WA [auth o], X [auth P], XA [auth p], Y [auth Q], Z [auth R]	129	Squalus acanthias	Mutation(s): 0 Gene Names: NAR
UniProt
Find proteins for Q8JGJ1 (Ginglymostoma cirratum) Explore Q8JGJ1 Go to UniProtKB: Q8JGJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JGJ1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	AA [auth S] AB [auth s] BA [auth T] C [auth 2] CA [auth U] AA [auth S], AB [auth s], BA [auth T], C [auth 2], CA [auth U], D [auth 3], E [auth 4], EB [auth w], FB [auth x], GA [auth Y], GB [auth y], HA [auth Z], I [auth A], IA [auth a], J [auth B], K [auth C], MA [auth e], NA [auth f], O [auth G], OA [auth g], P [auth H], Q [auth I], SA [auth k], TA [auth l], U [auth M], UA [auth m], V [auth N], W [auth O], YA [auth q], ZA [auth r]	156	Homo sapiens	Mutation(s): 0 Gene Names: TNF, TNFA, TNFSF2
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain NB [auth P] SDF format, chain WB [auth h] SDF format, chain ZB [auth t] MOL2 format, chain NB [auth P] MOL2 format, chain WB [auth h] MOL2 format, chain ZB [auth t] mmCIF format, chain NB [auth P] mmCIF format, chain WB [auth h] mmCIF format, chain ZB [auth t]	NB [auth P], WB [auth h], ZB [auth t]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain NB [auth P] Focus chain WB [auth h] Focus chain ZB [auth t] Interactions & Density Focus chain NB [auth P] Focus chain WB [auth h] Focus chain ZB [auth t]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AC [auth t] SDF format, chain BC [auth t] SDF format, chain CC [auth z] SDF format, chain IB [auth 0] SDF format, chain JB [auth 1] SDF format, chain KB [auth 5] SDF format, chain LB [auth D] SDF format, chain MB [auth J] SDF format, chain OB [auth P] SDF format, chain QB [auth V] SDF format, chain RB [auth W] SDF format, chain SB [auth b] SDF format, chain TB [auth b] SDF format, chain UB [auth b] SDF format, chain VB [auth c] SDF format, chain XB [auth h] SDF format, chain YB [auth n] MOL2 format, chain AC [auth t] MOL2 format, chain BC [auth t] MOL2 format, chain CC [auth z] MOL2 format, chain IB [auth 0] MOL2 format, chain JB [auth 1] MOL2 format, chain KB [auth 5] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth J] MOL2 format, chain OB [auth P] MOL2 format, chain QB [auth V] MOL2 format, chain RB [auth W] MOL2 format, chain SB [auth b] MOL2 format, chain TB [auth b] MOL2 format, chain UB [auth b] MOL2 format, chain VB [auth c] MOL2 format, chain XB [auth h] MOL2 format, chain YB [auth n] mmCIF format, chain AC [auth t] mmCIF format, chain BC [auth t] mmCIF format, chain CC [auth z] mmCIF format, chain IB [auth 0] mmCIF format, chain JB [auth 1] mmCIF format, chain KB [auth 5] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth J] mmCIF format, chain OB [auth P] mmCIF format, chain QB [auth V] mmCIF format, chain RB [auth W] mmCIF format, chain SB [auth b] mmCIF format, chain TB [auth b] mmCIF format, chain UB [auth b] mmCIF format, chain VB [auth c] mmCIF format, chain XB [auth h] mmCIF format, chain YB [auth n]	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		Interactions Focus chain AC [auth t] Focus chain BC [auth t] Focus chain CC [auth z] Focus chain IB [auth 0] Focus chain JB [auth 1] Focus chain KB [auth 5] Focus chain LB [auth D] Focus chain MB [auth J] Focus chain OB [auth P] Focus chain QB [auth V] Focus chain RB [auth W] Focus chain SB [auth b] Focus chain TB [auth b] Focus chain UB [auth b] Focus chain VB [auth c] Focus chain XB [auth h] Focus chain YB [auth n] Interactions & Density Focus chain AC [auth t] Focus chain BC [auth t] Focus chain CC [auth z] Focus chain IB [auth 0] Focus chain JB [auth 1] Focus chain KB [auth 5] Focus chain LB [auth D] Focus chain MB [auth J] Focus chain OB [auth P] Focus chain QB [auth V] Focus chain RB [auth W] Focus chain SB [auth b] Focus chain TB [auth b] Focus chain UB [auth b] Focus chain VB [auth c] Focus chain XB [auth h] Focus chain YB [auth n]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain PB [auth S] MOL2 format, chain PB [auth S] mmCIF format, chain PB [auth S]	PB [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain PB [auth S] Interactions & Density Focus chain PB [auth S]

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 = 112.32	α = 90
b = 218.127	β = 96.28
c = 236.485	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

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