21TW: TNF-alpha

Cryo-EM structure of TNF-alpha in complex with two anti-TNF-alpha nanobodies, TNF30, derived from the TNF-alpha inhibitor Ozoralizumab (OZR). Determined by electron microscopy at 2.43 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 2.43 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,979
Mol. weight: 90.75 kDa
Released: 29 Apr 2026

Explore 21TW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

21TW contains 5 α-helices and 65 β-strands across 4 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: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11	1	2
β-strand	18-20	3	3
β-strand	21-25	5	1
β-strand	32	1	4
β-strand	34-39	6	5
β-strand	46-51	6	5
β-strand	58-59	2	5
β-strand	68-69	2	3
β-strand	72-73	2	1
β-strand	78-79	2	1
β-strand	81-83	3	3
α-helix	88-90	3
β-strand	92-97	6	5
β-strand	109-111	3	5
β-strand	112	1	2
β-strand	251-254	4	6
β-strand	266-273	8	6
α-helix	277-279	3
β-strand	280	1	7
β-strand	282-287	6	8
β-strand	293-299	7	8
β-strand	306-307	2	8
β-strand	316-321	6	6
β-strand	326-331	6	6
α-helix	336-338	3
β-strand	341-345	5	8
β-strand	357-358	2	8

Chain B: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	9
β-strand	28-29	2	9
β-strand	37-38	2	9
β-strand	42-44	3	4
β-strand	47-49	3	4
β-strand	54-58	5	10
β-strand	59-67	9	9
β-strand	76-83	8	4
β-strand	90-98	9	4
β-strand	113-119	7	9
β-strand	122-126	5	10
β-strand	131-133	3	4
β-strand	136	1	4
α-helix	139-141	3
β-strand	142	1	9
β-strand	151-155	5	9
β-strand	156	1	10

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	11
β-strand	28-29	2	11
β-strand	37-38	2	11
β-strand	42-44	3	7
β-strand	47-49	3	7
β-strand	54-66	13	11
β-strand	76-83	8	7
β-strand	90-98	9	7
β-strand	114-126	13	11
β-strand	131-136	6	7
α-helix	139-141	3
β-strand	142	1	11
β-strand	151-155	5	11

Chain D: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-17	5	12
β-strand	29	1	12
β-strand	36-38	3	12
β-strand	42-43	2	13
β-strand	48-49	2	13
β-strand	54-66	13	12
β-strand	76-83	8	13
β-strand	90-98	9	13
β-strand	114-126	13	12
β-strand	131-136	6	13
β-strand	142	1	12
β-strand	151-156	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-TNF-alpha nanobodies, TNF30, derived from Ozoralizumab (OZR)	A	protein	363	Homo sapiens
Tumor necrosis factor	B, C, D	protein	158	Homo sapiens	P01375 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>21TW_1 anti-TNF-alpha nanobodies, TNF30, derived from Ozoralizumab (OZR) (chains A)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSDYWMYWVRQAPGKGLEWVSEINTNGLITKY
PDSVKGRFTISRDNAKNTLYLQMNSLRPEDTAVYYCARSPSGFNRGQGTLVTVSSGGGGS
GGGSEVQLVESGGGLVQPGNSLRLSCAASGFTFSSFGMSWVRQAPGKGLEWVSSISGSGS
DTLYADSVKGRFTISRDNAKTTLYLQMNSLRPEDTAVYYCTIGGSLSRSSQGTLVTVSSG
GGGSGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFSDYWMYWVRQAPGKGLEWVSEIN
TNGLITKYPDSVKGRFTISRDNAKNTLYLQMNSLRPEDTAVYYCARSPSGFNRGQGTLVT
VSS

Sequence of entity 2 (B, C, D), FASTA

>21TW_2 Tumor necrosis factor (chains B, C, D)
GVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIY
SQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIY
LGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Primary citation

Cryo-EM elucidates the interaction mechanism of ozoralizumab, a humanized anti-TNF alpha NANOBODY® compound. Mima, M., Sato, K., Yokoyama, T. et al. Biochem Biophys Res Commun (2026) 816:153572-153572. DOI 10.1016/j.bbrc.2026.153572 · 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
9BN7 1.92 Å, X-ray crystal structure of TNFa-VNAR C4 complex
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

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