8ZUK: TNF receptor-associated factor 3

Cluster structure of the BAFF-BAFFR-TRAF3 complex. Determined by electron microscopy at 2.83 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 42
Atoms: 32,550
Mol. weight: 1162.29 kDa
Released: 11 Jun 2025

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

Secondary structure: helices and β-sheets

8ZUK contains 126 α-helices and 294 β-strands across 42 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, A, B, C, e, f, g, G, H, I, k, l, m, M, N, O, S, T, U, Y and Z: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	388-409	22
β-strand	412	1	3
β-strand	416-422	7	4
α-helix	424-433	10
β-strand	438-440	3	3
α-helix	441-443	3
β-strand	444-445	2	3
β-strand	452-458	7	3
α-helix	463-465	3
β-strand	469-477	9	3
α-helix	482-484	3
β-strand	493-497	5	4
β-strand	507-511	5	4
β-strand	527	1	3
β-strand	531-538	8	3
α-helix	539-542	4
β-strand	549	1	4
β-strand	552-559	8	4

Chains b, c, d, D, E, F, h, i, j, J, K, L, n, o, p, P, Q, R, V, W and X: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	163-164	2	39
β-strand	171-173	3	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TNF receptor-associated factor 3	A, B, C, G, H, I, M, N, O, S, T, U, Y, Z, a, e, f, g, k, l, m	protein	310	Homo sapiens	Q13114 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 13C	D, E, F, J, K, L, P, Q, R, V, W, X, b, c, d, h, i, j, n, o, p	protein	193	Homo sapiens	Q96RJ3 (AlphaFold model)

Sequence of entity 1 (A, B, C, G, H, I, M, N, O, S, T, U, Y, Z, a, e, f, g, k, l, m), FASTA

>8ZUK_1 TNF receptor-associated factor 3 (chains A, B, C, G, H, I, M, N, O, S, T, U, Y, Z, a, e, f, g, k, l, m)
MSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDS
QAEKLKELDKEIRPFRQNWEEADSMKSSVESLQNRVTELESVDKSAGQVARNTGLLESQL
SRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPF
YTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSR
RHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDL
PDPGGSLVPR

Sequence of entity 2 (D, E, F, J, K, L, P, Q, R, V, W, X, b, c, d, h, i, j, n, o, p), FASTA

>8ZUK_2 Tumor necrosis factor receptor superfamily member 13C (chains D, E, F, J, K, L, P, Q, R, V, W, X, b, c, d, h, i, j, n, o, p)
MRRGPRSLRGRDAPAPTPCVPAECFDLLVRHCVACGLLRTPRPKPAGASSPAPRTALQPQ
ESVGAGAGEAALPLPGLLFGAPALLGLALVLALVLVGLVSWRRRQRRLRGASSAEAPDGD
KDAPEPLDKVIILSPGISDATAPAWPPPGEDPGTTPPGHSVPVPATELGSTELVTTKTAG
PEQQSNSLEVLFQ

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 Q13114 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8T5P 2.5 Å, SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain
2GKW 2.7 Å, Key contacts promote recongnito of BAFF-R by TRAF3
1FLK 2.8 Å, Molecular basis for CD40 signaling mediated by TRAF3
1ZMS 2.8 Å, LMP1 Protein binds to TRAF3 as a structural CD40
1L0A 2.9 Å, Downstream regulator tank binds to the CD40 recognition site on TRAF3
1FLL 3.5 Å, Molecular basis for CD40 signaling mediated by TRAF3
1KZZ 3.5 Å, Downstream regulator tank binds to the CD40 recognition site on TRAF3
1RF3 3.5 Å, Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for…
2ECY Solution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF…

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