8C7M: Interleukin-12 receptor subunit beta-1

Interleukin 12 receptor subunit beta-1 Fn domains in complex with antagonistic FAb fragment. Determined by X-ray diffraction at 2.56 Å resolution. Released 31 Jan 2024.

Method: X-ray diffraction
Resolution: 2.56 Å
Organisms: Homo sapiens, Homo sapiens x Mus musculus hybrid cell line
Chains: 6
Atoms: 10,911
Mol. weight: 165.74 kDa
Ligands: NAG
Released: 31 Jan 2024

Explore 8C7M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C7M contains 60 α-helices and 134 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: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	241-245	5	1
α-helix	246-248	3
β-strand	254-255	2	2
β-strand	256-260	5	1
β-strand	282-288	7	3
β-strand	298-301	4	3
β-strand	308-309	2	2
β-strand	314-320	7	3
β-strand	330-334	5	3
α-helix	335-336	2
β-strand	340	1	4
α-helix	344-345	2
β-strand	348-350	3	5
β-strand	353-359	7	5
β-strand	365	1	6
β-strand	366-373	8	4
β-strand	382-385	4	4
α-helix	386-388	3
β-strand	389	1	6
α-helix	390-392	3
β-strand	396-402	7	5
α-helix	403-405	3
β-strand	413-421	9	4
α-helix	427-429	3
β-strand	431-439	9	4
α-helix	443-446	4
β-strand	453-458	6	7
β-strand	461-465	5	7
α-helix	467-469	3
α-helix	470-473	4
β-strand	478-487	10	8
β-strand	493-498	6	8
β-strand	504-507	4	7
β-strand	515-524	10	8
α-helix	528-534	7
β-strand	535-538	4	8

Chain B: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	241-245	5	9
α-helix	246-248	3
β-strand	254-255	2	10
β-strand	256-260	5	9
β-strand	282-288	7	11
β-strand	298-301	4	11
β-strand	308-309	2	10
β-strand	314-320	7	11
β-strand	330-334	5	11
α-helix	335-336	2
β-strand	340	1	12
α-helix	344-345	2
β-strand	348-350	3	13
β-strand	353-359	7	13
β-strand	365	1	14
β-strand	366-373	8	12
β-strand	382-385	4	12
α-helix	386-388	3
β-strand	389	1	14
α-helix	390-392	3
β-strand	396-402	7	13
α-helix	403-405	3
β-strand	413-421	9	12
α-helix	427-429	3
β-strand	431-439	9	12
α-helix	443-446	4
β-strand	453-458	6	15
β-strand	461-465	5	15
α-helix	467-469	3
α-helix	470-473	4
β-strand	478-487	10	16
β-strand	493-498	6	16
β-strand	504-508	5	15
α-helix	510-511	2
β-strand	515-524	10	16
α-helix	528-534	7
β-strand	535-538	4	16

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-98	7	18
β-strand	110-111	2	18
β-strand	115-119	5	18
β-strand	125	1	19
α-helix	126-127	2
β-strand	128-132	5	20
α-helix	133-134	2
β-strand	143-153	11	20
β-strand	154	1	19
β-strand	159-162	4	21
α-helix	163-165	3
β-strand	171-173	3	20
α-helix	174-176	3
β-strand	177-178	2	20
β-strand	184-193	10	20
α-helix	194-196	3
β-strand	203-208	6	21
β-strand	213-218	6	21

Chain D: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
β-strand	9-12	4	23
β-strand	18-24	7	22
β-strand	32-37	6	23
β-strand	44-48	5	23
β-strand	52-53	2	23
α-helix	54	1
β-strand	61-66	6	22
β-strand	69-74	6	22
α-helix	79-81	3
β-strand	84-89	6	23
α-helix	95	1
β-strand	96-97	2	23
β-strand	101-105	5	23
α-helix	106	1
β-strand	110	1	24
α-helix	111-112	2
β-strand	113-117	5	25
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	25
β-strand	139	1	24
β-strand	144-149	6	26
β-strand	152-153	2	26
α-helix	154	1
β-strand	158-162	5	25
α-helix	163-166	4
β-strand	172-181	10	25
α-helix	182-187	6
β-strand	190-196	7	26
β-strand	201-207	7	26

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	27
β-strand	10-12	3	28
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	34-39	6	28
β-strand	45-51	7	28
β-strand	58-60	3	28
α-helix	62-64	3
β-strand	68-73	6	27
β-strand	78-83	6	27
α-helix	88-90	3
β-strand	92-98	7	28
β-strand	110-111	2	28
β-strand	115-119	5	28
β-strand	125	1	29
α-helix	126-127	2
β-strand	128-132	5	30
α-helix	133-135	3
β-strand	143-153	11	30
β-strand	154	1	29
β-strand	159-162	4	31
α-helix	163-165	3
β-strand	171-173	3	30
α-helix	174-176	3
β-strand	177-178	2	30
β-strand	184-193	10	30
α-helix	194-196	3
β-strand	202-208	7	31
α-helix	209-211	3
β-strand	213-219	7	31

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	32
β-strand	9-12	4	33
β-strand	18-24	7	32
β-strand	32-37	6	33
β-strand	44-48	5	33
β-strand	52-53	2	33
α-helix	54	1
β-strand	61-66	6	32
β-strand	69-74	6	32
α-helix	79-81	3
β-strand	84-89	6	33
α-helix	95	1
β-strand	96-97	2	33
β-strand	101-105	5	33
α-helix	106	1
β-strand	110	1	34
α-helix	111-112	2
β-strand	113-117	5	35
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	35
β-strand	139	1	34
β-strand	144-149	6	36
β-strand	152-153	2	36
α-helix	154	1
β-strand	158-162	5	35
α-helix	163-166	4
β-strand	172-181	10	35
α-helix	182-186	5
β-strand	190-197	8	36
β-strand	200-207	8	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 receptor subunit beta-1	A, B	protein	313	Homo sapiens	P42701 (AlphaFold model)
FAb4 Heavy chain	C, H	protein	231	Homo sapiens x Mus musculus hybrid cell line
FAb4 Crystal Kappa Light chain	D, L	protein	212	Homo sapiens x Mus musculus hybrid cell line

Sequence of entity 1 (A, B), FASTA

>8C7M_1 Interleukin-12 receptor subunit beta-1 (chains A, B)
PPENPPQPQVRFSVEQLGQDGRRRLTLKEQPTQLELPEGCQGLAPGTEVTYRLQLHMLSC
PCKAKATRTLHLGKMPYLSGAAYNVAVISSNQFGPGLNQTWHIPADTHTEPVALNISVGT
NGTTMYWPARAQSMTYCIEWQPVGQDGGLATCSLTAPQDPDPAGMATYSWSRESGAMGQE
KCYYITIFASAHPEKLTLWSTVLSTYHFGGNASAAGTPHHVSVKNHSLDSVSVDWAPSLL
STCPGVLKEYVVRCRDEDSKQVSEHPVQPTETQVTLSGLRAGVAYTVQVRADTAWLRGVW
SQPQRFSIEDEVD

Sequence of entity 2 (C, H), FASTA

>8C7M_2 FAb4 Heavy chain (chains C, H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFTSYGMSWVRQAPGKGLEWVAGISYDASDTEY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARSPDYIIDYGFDYWGRGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGHHHHHH

Sequence of entity 3 (D, L), FASTA

>8C7M_3 FAb4 Crystal Kappa Light chain (chains D, L)
AIQMTQSPSSLSASVGDRVTITCRASQGISSDLAWYQQKPGKAPKLLIYDASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYWWYPFTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Water and common crystallization additives (CL) are not listed.

Primary citation

Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23. Bloch, Y., Felix, J., Merceron, R. et al. Nat Struct Mol Biol (2024) 31:591-597. DOI 10.1038/s41594-023-01190-6 · PubMed

Other PDB entries of the same protein (UniProt P42701 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WDP 2.01 Å, Interleukin 12 receptor subunit beta-1
6WDQ 3.4 Å, IL23/IL23R/IL12Rb1 signaling complex
8YI7 3.57 Å, The Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2…
8OE4 3.6 Å, Cryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex.
8XRP 3.75 Å, The Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2…
8ODX 4.4 Å, Interleukin 12 receptor subunit beta-1 Fn domains in complex with antagonistic FAb4…

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