5MJ4: Interleukin-12 subunit beta

Interleukin-23 complex with an antagonistic alphabody, crystal form 2. Determined by X-ray diffraction at 3.4 Å resolution. Released 11 Jan 2017.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 4,115
Mol. weight: 67.35 kDa
Released: 11 Jan 2017

Explore 5MJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MJ4 contains 17 α-helices and 26 β-strands across 3 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: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	30-36	7	1
β-strand	44-49	6	2
β-strand	58-62	5	1
β-strand	70-71	2	1
β-strand	74-79	6	2
α-helix	82-84	3
β-strand	86-92	7	1
β-strand	95-108	14	1
β-strand	111-112	2	1
α-helix	118-119	2
β-strand	130-132	3	1
β-strand	133	1	3
β-strand	139-146	8	1
β-strand	152-160	9	1
α-helix	165	1
β-strand	166-170	5	1
β-strand	174-178	5	1
β-strand	187-195	9	1
β-strand	208-216	9	1
β-strand	219-227	9	1
α-helix	229-232	4
β-strand	233	1	3
α-helix	235-238	4
β-strand	239-244	6	4
β-strand	253-257	5	4
β-strand	271-277	7	5
β-strand	287-291	5	5
β-strand	295-297	3	4
β-strand	306-312	7	5
α-helix	318-322	5
β-strand	323-325	3	5

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	30-46	17
α-helix	61-64	4
α-helix	65-67	3
α-helix	79-104	26
α-helix	107-110	4
α-helix	114-116	3
α-helix	120-135	16
α-helix	155-186	32

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-26	23
α-helix	48-69	22
α-helix	92-116	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 subunit beta	A	protein	306	Homo sapiens	P29460 (AlphaFold model)
Interleukin-23 subunit alpha	B	protein	179	Homo sapiens	Q9NPF7 (AlphaFold model)
Alphabody MA12	C	protein	118	synthetic construct

Sequence of entity 1 (A), FASTA

>5MJ4_1 Interleukin-12 subunit beta (chains A)
IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEF
GDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTC
WWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAA
EESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTW
STPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEW
ASVPCS

Sequence of entity 2 (B), FASTA

>5MJ4_2 Interleukin-23 subunit alpha (chains B)
RAVPGGSSPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEGDEETTNDVPHIQCGDGCDP
QGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSPVGQLHASLLGLSQLLQPEG
HHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVFAHGAATLSPGTKHHHHHH

Sequence of entity 3 (C), FASTA

>5MJ4_3 ALPHABODY MA12 (chains C)
HMSIQEIQKEIAQIQAVIAGIQKYIYTMTGGSGGSGGGGSGGSGGMSIEEIQKQIAAIQC
QIAAIQKQIYAMTGSGGGGSGGSGGGGSGMSIEEIQKQIAAIQEQILAIYKQIMAMVT

Primary citation

STRUCTURAL BASIS OF IL-23 ANTAGONISM BY AN ALPHABODY PROTEIN. Desmet, J., Verstraete, K., Bloch, Y. et al. Nature Communications (2014) 5:5237. DOI 10.1038/NCOMMS6237 · PubMed

Other PDB entries of the same protein (UniProt P29460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MJ3 1.74 Å, Interleukin-23 complex with an antagonistic alphabody, crystal form 1
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
8CR8 2.0 Å, human Interleukin-23
3DUH 2.3 Å, Structure of Interleukin-23
8UUI 2.43 Å, X-ray structure of Interleukin-23 in complex with peptide 23-446
1F42 2.5 Å, The P40 domain of human interleukin-12
5MXA 2.5 Å, Structure of unbound Interleukin-23
4GRW 2.55 Å, Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs)
6UIB 2.74 Å, Crystal structure of IL23 bound to peptide 23-652
1F45 2.8 Å, Human interleukin-12
5MZV 2.8 Å, IL-23:IL-23R:Nb22E11 complex
3D87 2.9 Å, Crystal structure of Interleukin-23

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