5MZV: IL-23:IL-23R:Nb22E11 complex

Name: PDB 5MZV: IL-23:IL-23R:Nb22E11 complex
Published: 2018-01-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

IL-23:IL-23R:Nb22E11 complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 3 Jan 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 7,116
Mol. weight: 117.96 kDa
Ligands: NAG
Released: 3 Jan 2018

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

Secondary structure: helices and β-sheets

5MZV contains 20 α-helices and 64 β-strands across 4 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: 4 helices, 27 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	71	1	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
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	174-181	8	1
β-strand	184-195	12	1
β-strand	208-216	9	1
β-strand	219-227	9	1
α-helix	229-231	3
β-strand	233	1	3
α-helix	235-238	4
β-strand	239-242	4	4
β-strand	245	1	4
β-strand	251-257	7	4
β-strand	271-278	8	5
β-strand	288-291	4	5
β-strand	295-299	5	4
β-strand	305-312	8	5
β-strand	323-326	4	5

Chain B: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	30-47	18
β-strand	56-57	2	6
α-helix	79-84	6
α-helix	86-104	19
α-helix	107-110	4
α-helix	114-116	3
α-helix	121-133	13
α-helix	152-154	3
α-helix	155-186	32

Chain C: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	7
β-strand	41-43	3	6
β-strand	48-54	7	7
β-strand	64-68	5	6
β-strand	71-72	2	6
β-strand	77-81	5	7
β-strand	84-89	6	7
β-strand	96-104	9	6
β-strand	111-122	12	6
α-helix	124-126	3
β-strand	129-134	6	8
β-strand	135-136	2	9
β-strand	141-147	7	8
β-strand	157-164	8	10
β-strand	170-175	6	10
β-strand	179-182	4	8
α-helix	183-185	3
β-strand	191-200	10	10
β-strand	203-206	4	10
α-helix	207-209	3
β-strand	210-213	4	10
β-strand	218-219	2	9
α-helix	220-222	3
β-strand	223-230	8	11
α-helix	236	1
β-strand	237-244	8	11
β-strand	251-259	9	12
β-strand	266-270	5	12
β-strand	278-283	6	11
β-strand	290-298	9	12
α-helix	305-310	6

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	18-24	7	13
β-strand	33-39	7	14
β-strand	46-52	7	14
β-strand	59-60	2	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	14
α-helix	107-109	3
β-strand	110-113	4	14
β-strand	117-122	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 subunit beta	A	protein	328	Homo sapiens	P29460 (AlphaFold model)
Interleukin-23 subunit alpha	B	protein	198	Homo sapiens	Q9NPF7 (AlphaFold model)
Interleukin-23 receptor	C	protein	330	Homo sapiens	Q5VWK5 (AlphaFold model)
Nanobody 22E11	D	protein	156	Lama glama

Sequence of entity 1 (A), FASTA

>5MZV_1 Interleukin-12 subunit beta (chains A)
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITW
TLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQ
KEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERV
RGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKN
LQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVIC
RKNASISVRAQDRYYSSSWSEWASVPCS

Sequence of entity 2 (B), FASTA

>5MZV_2 Interleukin-23 subunit alpha (chains B)
MLGSRAVMLLLLLPWTAQGRAVPGGSSPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEG
DEETTNDVPHIQCGDGCDPQGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSP
VGQLHASLLGLSQLLQPEGHHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVF
AHGAATLSPGTKHHHHHH

Sequence of entity 3 (C), FASTA

>5MZV_3 Interleukin-23 receptor (chains C)
MNQVTIQWDAVIALYILFSWCHGGITNINCSGHIWVEPATIFKMGMNISIYCQAAIKNCQ
PRKLHFYKNGIKERFQITRINKTTARLWYKNFLEPHASMYCTAECPKHFQETLICGKDIS
SGYPPDIPDEVTCVIYEYSGNMTCTWNAGKLTYIDTKYVVHVKSLETEEEQQYLTSSYIN
ISTDSLQGGKKYLVWVQAANALGMEESKQLQIHLDDIVIPSAAVISRAETINATVPKTII
YWDSQTTIEKVSCEMRYKATTNQTWNVKEFDTNFTYVQQSEFYLEPNIKYVFQVRCQETG
KRYWQPWSSLFFHKTPEIEGRGTKHHHHHH

Sequence of entity 4 (D), FASTA

>5MZV_4 Nanobody 22E11 (chains D)
MKYLLPTAAAGLLLLAAQPAMAEVQLVESGGGLVQAGGSLRLSCAASGRTFSWSAVGWFR
QAPGKEREFVAAIRWSGGSPYYADSVKDRFTISRDNAKNTVYLQMNSLRPEDTAVYLCGE
TSLFPTSRGSHYDTWGQGTQVTVSSGSGWSHPQFEK

Ligands and cofactors

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

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

Primary citation

Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12R beta 1. Bloch, Y., Bouchareychas, L., Merceron, R. et al. Immunity (2018) 48:45-58.e6. DOI 10.1016/j.immuni.2017.12.008 · 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
3D87 2.9 Å, Crystal structure of Interleukin-23
3HMX 3.0 Å, Crystal structure of ustekinumab FAB/IL-12 complex

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