4V46: BAFF-BAFF-R complex

Crystal structure of the BAFF-BAFF-R complex. Determined by X-ray diffraction at 3.3 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 120
Atoms: 79,720
Mol. weight: 1406.71 kDa
Ligands: MG
Released: 9 Jul 2014

Explore 4V46 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V46 contains 180 α-helices and 900 β-strands across 120 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 A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, Aa, AA, Ab, AB, Ac, AC, Ad, AD, Ae, AE, Af, AF, Ag, AG, Ah, AH, Ai, AI, Aj, AJ, Ak, AK, Al, AL, Am, AM, An, AN, Ao, AO, Ap, AP, Aq, AQ, Ar, AR, As, AS, At, AT, Au, AU, Av, AV, Aw, AW, Ax, AX, AY and AZ: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	3
α-helix	156-157	2
β-strand	158-159	2	4
β-strand	164-165	2	4
β-strand	168-174	7	3
β-strand	178-181	4	4
β-strand	184-187	4	4
β-strand	191-201	11	3
β-strand	207-215	9	4
β-strand	226-235	10	4
β-strand	243-253	11	3
β-strand	258-263	6	4
β-strand	270	1	3
β-strand	278-283	6	3

Chains B0, B1, B2, B4, B5, B6, B7, B8, Ba, Bb, Bc, Bd, BD, Be, BE, Bf, BF, Bg, BG, Bh, BH, Bi, BI, Bj, BK, BL, Bm, BM, Bn, Bo, BO, BP, Bq, BQ, Br, BR, Bs, BS, Bt, BT, Bu, Bv, Bw, BY and BZ: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
β-strand	23-26	4	70
β-strand	31-34	4	70
α-helix	35-37	3

Chains B3, B9, BA, BB, BC, BJ, Bk, Bl, BN, Bp, BU, BV, BW, Bx and BX: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
β-strand	24-26	3	91
β-strand	31-33	3	91
α-helix	35-37	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor ligand superfamily member 13B	A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax	protein	148	Homo sapiens	Q9Y275 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 13C	B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, Ba, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Br, Bs, Bt, Bu, Bv, Bw, Bx	protein	63	Homo sapiens	Q96RJ3 (AlphaFold model)

Sequence of entity 1 (A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax), FASTA

>4V46_1 Tumor necrosis factor ligand superfamily member 13B (chains A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax)
PEETVTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYG
QVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGD
ELQLAIPRENAQISLDGDVTFFGALKLL

Sequence of entity 2 (B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, Ba, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Br, Bs, Bt, Bu, Bv, Bw, Bx), FASTA

>4V46_2 Tumor necrosis factor receptor superfamily member 13C (chains B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, Ba, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Br, Bs, Bt, Bu, Bv, Bw, Bx)
MRRGPRSLRGRDAPAPTPCVPAECFDLLVRHCVACGLLRTPRPKPAGASSPAPRTALQPQ
ESV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	40

Primary citation

Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation. Kim, H.M., Yu, K.S., Lee, M.E. et al. Nat Struct Biol (2003) 10:342-348. DOI 10.1038/nsb925 · PubMed

Other PDB entries of the same protein (UniProt Q9Y275 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KXG 2.0 Å, The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator.
5Y9J 2.05 Å, BAFF in complex with belimumab
4ZCH 2.43 Å, Single-chain human APRIL-BAFF-BAFF Heterotrimer
1OQE 2.5 Å, Crystal structure of sTALL-1 with BAFF-R
8ZUJ 2.58 Å, Pentagonal cluster of BAFF-BAFFR ectodomain complex
1OQD 2.6 Å, Crystal structure of sTALL-1 and BCMA
1KD7 2.8 Å, Crystal structure of an extracellular domain fragment of human BAFF
6FXN 2.9 Å, Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody…
1JH5 3.0 Å, Crystal Structure of sTALL-1 of TNF family ligand
1OSG 3.0 Å, Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold
3V56 3.0 Å, Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide…

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