6FXN: Human BAFF

Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab. Determined by X-ray diffraction at 2.9 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 18
Atoms: 26,179
Mol. weight: 389.19 kDa
Released: 4 Apr 2018

Explore 6FXN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FXN contains 88 α-helices and 353 β-strands across 18 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: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	1
β-strand	158-160	3	2
β-strand	163-165	3	2
α-helix	166-167	2
β-strand	168-174	7	1
β-strand	178-181	4	2
β-strand	184-187	4	2
β-strand	191-201	11	1
β-strand	207-215	9	2
β-strand	226-235	10	2
β-strand	243-253	11	1
β-strand	258-263	6	2
β-strand	270-271	2	1
β-strand	278-283	6	1

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	3
α-helix	156-157	2
β-strand	158-160	3	4
β-strand	163-165	3	4
α-helix	166-167	2
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

Chain C: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	146-151	6	5
β-strand	158-160	3	6
β-strand	163-165	3	6
β-strand	168-174	7	5
β-strand	178-181	4	6
β-strand	184-187	4	6
β-strand	191-201	11	5
β-strand	207-215	9	6
β-strand	226-235	10	6
β-strand	243-253	11	5
β-strand	258-263	6	6
β-strand	270	1	5
β-strand	278-283	6	5

Chain D: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
β-strand	34-39	6	8
β-strand	45-51	7	8
α-helix	57-58	2
β-strand	59-60	2	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-97	6	8
β-strand	113	1	8
β-strand	117-121	5	8
α-helix	125-126	2
β-strand	127	1	9
β-strand	130-134	5	10
β-strand	146-155	10	10
β-strand	156	1	9
β-strand	161-164	4	11
α-helix	165-167	3
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-180	2	10
β-strand	186-194	9	10
β-strand	199	1	12
β-strand	202	1	12
β-strand	205-210	6	11
β-strand	215-220	6	11

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	13
β-strand	9-13	5	14
β-strand	18-23	6	13
α-helix	25-28	4
β-strand	33-37	5	14
β-strand	44-48	5	14
β-strand	52	1	14
α-helix	53-54	2
β-strand	61-66	6	13
β-strand	69-74	6	13
α-helix	79-81	3
β-strand	84-89	6	14
β-strand	98-99	2	14
β-strand	103-108	6	14
α-helix	110-112	3
β-strand	113	1	15
α-helix	114-115	2
β-strand	116-120	5	16
α-helix	124-128	5
β-strand	132-141	10	16
β-strand	142	1	15
β-strand	147-152	6	17
β-strand	155-156	2	17
β-strand	161-163	3	16
α-helix	164-166	3
β-strand	167-168	2	16
β-strand	174-182	9	16
α-helix	184-189	6
β-strand	193-199	7	17
β-strand	202-208	7	17

Chain F: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	18
α-helix	7-9	3
β-strand	10-12	3	19
β-strand	18-24	7	18
β-strand	33-39	7	19
β-strand	46-51	6	19
β-strand	59-60	2	19
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	113	1	19
β-strand	117-121	5	19
α-helix	125-126	2
β-strand	127	1	20
α-helix	128-129	2
β-strand	130-134	5	21
β-strand	145-155	11	21
β-strand	156	1	20
β-strand	161-164	4	22
β-strand	173-175	3	21
α-helix	176-178	3
β-strand	179-180	2	21
α-helix	181	1
β-strand	186-195	10	21
α-helix	196-198	3
β-strand	204-210	7	22
β-strand	215-221	7	22

Chain G: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	23
β-strand	9-13	5	24
β-strand	18-23	6	23
α-helix	25-28	4
β-strand	33-37	5	24
β-strand	44-47	4	24
β-strand	48	1	25
β-strand	52	1	25
β-strand	61-66	6	23
β-strand	69-74	6	23
α-helix	79-81	3
β-strand	84-89	6	24
β-strand	98-99	2	24
β-strand	103-108	6	24
α-helix	110-112	3
β-strand	113	1	26
α-helix	114-115	2
β-strand	116-120	5	27
α-helix	124-128	5
β-strand	132-141	10	27
β-strand	142	1	26
β-strand	147-152	6	28
β-strand	155-156	2	28
β-strand	161-163	3	27
α-helix	164-166	3
β-strand	167-168	2	27
β-strand	174-182	9	27
α-helix	184-189	6
β-strand	193-199	7	28
β-strand	202-208	7	28

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	29
α-helix	7-9	3
β-strand	10-12	3	30
β-strand	18-19	2	29
β-strand	22-24	3	29
β-strand	32-39	8	30
β-strand	45-51	7	30
β-strand	59-60	2	30
α-helix	62-64	3
β-strand	68-73	6	29
β-strand	78-83	6	29
α-helix	88-90	3
β-strand	92-100	9	30
β-strand	113	1	30
β-strand	117-121	5	30
α-helix	125-126	2
β-strand	127	1	31
α-helix	128-129	2
β-strand	130-134	5	32
β-strand	146-155	10	32
β-strand	156	1	31
β-strand	161-164	4	33
β-strand	173-175	3	32
α-helix	176-178	3
β-strand	179-180	2	32
β-strand	186-194	9	32
β-strand	204-210	7	33
α-helix	211-213	3
β-strand	215-221	7	33

10 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor ligand superfamily member 13B	A, B, C, J, K, L	protein	164	Homo sapiens	Q9Y275 (AlphaFold model)
belimumab heavy chain	D, F, H, M, O, Q	protein	225	Homo sapiens
belimumab light chain	E, G, I, N, P, R	protein	214	Homo sapiens

Sequence of entity 1 (A, B, C, J, K, L), FASTA

>6FXN_1 Tumor necrosis factor ligand superfamily member 13B (chains A, B, C, J, K, L)
MRGSHHHHHHGSAVQGPEETVTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEK
ENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVAVFGDELSLVTLFRCIQNMPETLP
NNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL

Sequence of entity 2 (D, F, H, M, O, Q), FASTA

>6FXN_2 belimumab heavy chain (chains D, F, H, M, O, Q)
QVQLQQSGAEVKKPGSSVRVSCKASGGTFNNNAINWVRQAPGQGLEWMGGIIPMFGTAKY
SQNFQGRVAITADESTGTASMELSSLRSEDTAVYYCARSRDLLLFPHHALSPWGRGTMVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 3 (E, G, I, N, P, R), FASTA

>6FXN_3 belimumab light chain (chains E, G, I, N, P, R)
SSELTQDPAVSVALGQTVRVTCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDR
FSGSSSGNTASLTITGAQAEDEADYYCSSRDSSGNHWVFGGGTELTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

A loop region of BAFF controls B cell survival and regulates recognition by different inhibitors. Vigolo, M., Chambers, M.G., Willen, L. et al. Nat Commun (2018) 9:1199-1199. DOI 10.1038/s41467-018-03323-8 · 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
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…
4V46 3.3 Å, Crystal structure of the BAFF-BAFF-R complex

Browse structure collections

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