8Y31: QX006N-Fab/IFNAR1-SD123 complex

The crystal structure of the QX006N-Fab/IFNAR1-SD123 complex. Determined by X-ray diffraction at 2.68 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,330
Mol. weight: 174.97 kDa
Released: 4 Dec 2024

Explore 8Y31 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y31 contains 40 α-helices and 115 β-strands across 6 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: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	29	1	3
β-strand	31	1	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	100-102	3	2
β-strand	106-111	6	2
β-strand	115	1	4
α-helix	116-117	2
β-strand	118-122	5	5
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	5
β-strand	144	1	4
β-strand	149-154	6	6
β-strand	157-158	2	6
β-strand	163-167	5	5
α-helix	168-171	4
β-strand	177-186	10	5
α-helix	187-191	5
β-strand	195-202	8	6
β-strand	205-212	8	6

Chain B: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	45-51	7	9
β-strand	57-59	3	9
α-helix	61-64	4
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-99	9	9
β-strand	105-109	5	9
β-strand	113-115	3	9
β-strand	116-117	2	8
α-helix	121-122	2
β-strand	123	1	10
α-helix	124-125	2
β-strand	126-130	5	11
β-strand	137	1	11
β-strand	141-151	11	11
β-strand	152	1	10
β-strand	157-160	4	12
α-helix	161-163	3
β-strand	165	1	12
β-strand	169-171	3	11
α-helix	172-174	3
β-strand	175-176	2	11
β-strand	182-191	10	11
α-helix	192-194	3
β-strand	195	1	13
β-strand	198	1	13
β-strand	200-206	7	12
α-helix	207-209	3
β-strand	211-217	7	12

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-91	8	15
β-strand	100-102	3	15
β-strand	106-111	6	15
β-strand	115	1	16
α-helix	116-117	2
β-strand	118-122	5	17
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	17
β-strand	144	1	16
β-strand	149-154	6	18
β-strand	157-158	2	18
β-strand	163-167	5	17
α-helix	168-171	4
β-strand	177-186	10	17
α-helix	187-191	5
β-strand	195-202	8	18
β-strand	205-212	8	18

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	33-39	7	21
β-strand	45-51	7	21
β-strand	57-59	3	21
α-helix	61-63	3
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	87-89	3
β-strand	91-99	9	21
β-strand	105-109	5	21
β-strand	113-115	3	21
β-strand	116-117	2	20
α-helix	121-122	2
β-strand	123	1	22
α-helix	124-125	2
β-strand	126-130	5	23
β-strand	137-138	2	23
β-strand	141-151	11	23
β-strand	152	1	22
β-strand	157-160	4	24
α-helix	161-163	3
β-strand	169-171	3	23
α-helix	172-174	3
β-strand	175-176	2	23
β-strand	182-191	10	23
α-helix	192-194	3
β-strand	200-206	7	24
α-helix	207-209	3
β-strand	211-217	7	24

Chains E and F: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	229	1	25
α-helix	230-232	3
β-strand	233-240	8	26
β-strand	243-249	7	26
β-strand	256-263	8	27
α-helix	264-267	4
β-strand	278-279	2	27
β-strand	286	1	27
β-strand	290-294	5	26
α-helix	295-297	3
β-strand	302-310	9	27
β-strand	315	1	27
β-strand	316	1	25
α-helix	317-321	5
β-strand	322-325	4	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
QX006N-Fab-LC	A, C	protein	216	Homo sapiens
QX006N-Fab-HC	B, D	protein	230	Homo sapiens
Interferon alpha/beta receptor 1	E, F	protein	346	Homo sapiens	P17181 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8Y31_1 QX006N-Fab-LC (chains A, C)
AIQMTQSPSSLSASVGDRVTITCQASQSISNQLSWYQQKPGKAPKLLIYDASSLASGVPS
RFSGSRSGTKFTLTISSLQPEDFATYYCLGIYGDGADDGIAFGGGTKVEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>8Y31_2 QX006N-Fab-HC (chains B, D)
EVQLVESGGGLVQPGGSLRLSCAASGFSLSSYYMTWVRQAPGKGLEWVSVINVYGGTYYA
SWAKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREDVAVYMAIDLWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGHHHHHH

Sequence of entity 3 (E, F), FASTA

>8Y31_3 Interferon alpha/beta receptor 1 (chains E, F)
MMVVLLGATTLVLVAVAPWVLSAAAGGKNLKSPQKVEVDIIDDNFILRWNRSDESVGNVT
FSFDYQKTGMDNWIKLSGCQNITSTKCNFSSLKLNVYEEIKLRIRAEKENTSSWYEVDSF
TPFRKAQIGPPEVHLEAEDKAIVIHISPGTKDSVMWALDGLSFTYSLVIWKNSSGVEERI
ENIYSRHKIYKLSPETTYCLKVKAALLTSWKIGVYSPVHCIKTTVENELPPPENIEVSVQ
NQNYVLKWDYTYANMTFQVQWLHAFLKRNPGNHLYKWKQIPDCENVKTTQCVFPQNVFQK
GIYLLRVQASDGNNTSFWSEEIKFDTEIQAFLLEVLFQGPHHHHHH

Primary citation

Structural basis for the recognition of IFNAR1 by the humanized therapeutic monoclonal antibody QX006N for the treatment of systemic lupus erythematosus. Chen, X., Ke, H., Li, W. et al. Int J Biol Macromol (2024) 268:131721-131721. DOI 10.1016/j.ijbiomac.2024.131721 · PubMed

Other PDB entries of the same protein (UniProt P17181 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3S98 1.9 Å, human IFNAR1
4PO6 1.99 Å, Crystal structure of the human TYK2 FERM and SH2 domains with an IFNAR1 intracellular…
3SE4 3.5 Å, human IFNw-IFNAR ternary complex
3SE3 4.0 Å, human IFNa2-IFNAR ternary complex

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