9BN7: TNFa-VNAR C4 complex

X-ray crystal structure of TNFa-VNAR C4 complex. Determined by X-ray diffraction at 1.92 Å resolution. Released 5 Nov 2025.

Method: X-ray diffraction
Resolution: 1.92 Å
Organisms: Homo sapiens, Squalus acanthias
Chains: 6
Atoms: 6,397
Mol. weight: 92.22 kDa
Ligands: NI
Released: 5 Nov 2025

Explore 9BN7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BN7 contains 11 α-helices and 69 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	36-38	3	1
β-strand	42-44	3	2
β-strand	47-49	3	2
β-strand	54-66	13	1
β-strand	76-83	8	2
β-strand	90-98	9	2
α-helix	104-106	3
β-strand	114-126	13	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
β-strand	151-156	6	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	3
β-strand	28-29	2	3
β-strand	36-38	3	3
β-strand	42-44	3	4
β-strand	47-49	3	4
β-strand	54-66	13	3
β-strand	76-83	8	4
β-strand	90-98	9	4
α-helix	104-106	3
α-helix	109-111	3
β-strand	114-126	13	3
β-strand	131-136	6	4
α-helix	139-141	3
β-strand	142	1	3
β-strand	151-156	6	3

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	5
β-strand	28-29	2	5
β-strand	36-38	3	5
β-strand	42-44	3	6
β-strand	47-49	3	6
β-strand	54-66	13	5
β-strand	76-83	8	6
β-strand	90-98	9	6
α-helix	104-106	3
α-helix	110-111	2
β-strand	114-126	13	5
β-strand	131-136	6	6
α-helix	139-141	3
β-strand	142	1	5
β-strand	151-156	6	5

Chains D, E and F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	9-13	5	8
β-strand	18-25	8	7
β-strand	33-40	8	8
β-strand	47-48	2	8
β-strand	52	1	7
β-strand	55-60	6	7
β-strand	65-70	6	7
α-helix	75-77	3
β-strand	79-86	8	8
β-strand	99-100	2	8
β-strand	104-109	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C	protein	157	Homo sapiens	P01375 (AlphaFold model)
VNARC4	D, E, F	protein	115	Squalus acanthias

Sequence of entity 1 (A, B, C), FASTA

>9BN7_1 Tumor necrosis factor (chains A, B, C)
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYL
GGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (D, E, F), FASTA

>9BN7_2 VNARC4 (chains D, E, F)
ARVDQTPQTITKETGESLTINCVLRDSNCGLSSTYWYRKKSGSTNEESISKGGRYVETIN
EGSKSFSLRINDLTVEDSGTYRCKLSWWTQNWRCSNSDVYGGGTVVTVNHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	4

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

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. et al. Nat Commun (2025) 17:256-256. DOI 10.1038/s41467-025-66967-3 · PubMed

Other PDB entries of the same protein (UniProt P01375 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OJO 1.36 Å, Crystal structure of TNF alpha in complex with compound 1
5UUI 1.4 Å, Crystal Structure of Spin-Labeled T77C TNFa
4Y6O 1.6 Å, Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
2E7A 1.8 Å, TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity
4TSV 1.8 Å, High resolution crystal structure of a human tnf-alpha mutant
9OJS 1.85 Å, Crystal structure of TNF alpha in complex with compound 4
5M2J 1.9 Å, Complex between human TNF alpha and Llama VHH2
2AZ5 2.1 Å, Crystal Structure of TNF-alpha with a small molecule inhibitor
3L9J 2.1 Å, Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal…
7JRA 2.1 Å, HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}qui…
5M2I 2.15 Å, Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1
7KP9 2.15 Å, asymmetric hTNF-alpha

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