8ZUI: Binary cluster of TNF-TNFR1 ectodomain complex

Binary cluster of TNF-TNFR1 ectodomain complex. Determined by electron microscopy at 2.56 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.56 Å
Organism: Homo sapiens
Chains: 12
Atoms: 13,378
Mol. weight: 246.28 kDa
Released: 11 Jun 2025

Explore 8ZUI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZUI contains 46 α-helices and 170 β-strands across 12 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.

Chains A, B, C, G, H and I: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	89-94	6	1
β-strand	104-105	2	1
β-strand	112-114	3	1
β-strand	118-120	3	2
β-strand	123-125	3	2
β-strand	130-143	14	1
β-strand	152-159	8	2
β-strand	166-174	9	2
β-strand	189-202	14	1
β-strand	207-212	6	2
α-helix	215-217	3
β-strand	218	1	1
β-strand	227-232	6	1

Chains D and K: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	48-50	3	7
β-strand	58-60	3	7
α-helix	61	1
β-strand	62	1	8
β-strand	66-70	5	9
α-helix	77-79	3
β-strand	80-83	4	9
β-strand	88-89	2	10
β-strand	94	1	8
α-helix	99	1
β-strand	100-101	2	10
α-helix	102-103	2
β-strand	112-115	4	11
α-helix	122-123	2
β-strand	124-126	3	11
β-strand	131-135	5	12
β-strand	141-145	5	12
β-strand	152-156	5	13
α-helix	163-164	2
β-strand	165-168	4	13
β-strand	172-175	4	14
β-strand	178-181	4	14

Chains E and J: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	48-50	3	15
β-strand	58-60	3	15
α-helix	61	1
β-strand	62	1	16
β-strand	66-70	5	17
α-helix	77-79	3
β-strand	80-83	4	17
β-strand	88-89	2	18
β-strand	94	1	16
α-helix	99	1
β-strand	100-101	2	18
α-helix	102-103	2
β-strand	112-115	4	19
α-helix	122-123	2
β-strand	124-126	3	19
β-strand	131-135	5	20
β-strand	141-145	5	20
α-helix	146-149	4
β-strand	152-156	5	21
α-helix	163-164	2
β-strand	165-168	4	21
β-strand	172-175	4	22
β-strand	178-181	4	22

Chains F and L: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	44-45	2
β-strand	48-50	3	23
β-strand	58-60	3	23
α-helix	61	1
β-strand	62	1	24
β-strand	66-70	5	25
β-strand	77	1	26
α-helix	78-79	2
β-strand	80-83	4	25
β-strand	88-89	2	27
β-strand	94	1	24
α-helix	99	1
β-strand	100-101	2	27
α-helix	102-103	2
β-strand	112-115	4	28
α-helix	122-123	2
β-strand	124-126	3	28
β-strand	131-135	5	29
β-strand	141-145	5	29
β-strand	152-156	5	30
α-helix	163-164	2
β-strand	165-168	4	30
β-strand	172-175	4	31
β-strand	178-181	4	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C, G, H, I	protein	170	Homo sapiens	P01375 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 1A, membrane form	D, E, F, J, K, L	protein	198	Homo sapiens	P19438 (AlphaFold model)

Sequence of entity 1 (A, B, C, G, H, I), FASTA

>8ZUI_1 Tumor necrosis factor (chains A, B, C, G, H, I)
ADPVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYL
IYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEP
IYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIALEFRSGRLVPR

Sequence of entity 2 (D, E, F, J, K, L), FASTA

>8ZUI_2 Tumor necrosis factor receptor superfamily member 1A, membrane form (chains D, E, F, J, K, L)
ADPLVPHLGDREKRDSVCPQGKYIHPQNNSICCTKCHKGTYLYNDCPGPGQDTDCRECES
GSFTASENHLRHCLSCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNC
SLCLNGTVHLSCQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIENVKGTE
DSGTTGGGGSHHHHHHHH

Primary citation

Highly ordered clustering of TNF alpha and BAFF ligand-receptor-intracellular adaptor complexes on a lipid membrane. Lim, C.S., Lee, J., Kim, J.W. et al. Nat Commun (2025) 16:5551-5551. DOI 10.1038/s41467-025-61271-6 · 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

Browse structure collections

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