4GRW: Complex of human IL-23 with 3 Nanobodies

Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs). Determined by X-ray diffraction at 2.55 Å resolution. Released 19 Feb 2014.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Homo sapiens, Lama glama
Chains: 10
Atoms: 13,131
Mol. weight: 199 kDa
Released: 19 Feb 2014

Explore 4GRW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GRW contains 53 α-helices and 118 β-strands across 10 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-28	18
α-helix	54-56	3
α-helix	60-66	7
α-helix	68-85	18
α-helix	88-91	4
α-helix	95-97	3
α-helix	101-116	16
α-helix	140-167	28

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	8-14	7	1
β-strand	22-27	6	2
β-strand	37-40	4	1
β-strand	48-49	2	1
β-strand	52-57	6	2
α-helix	60-62	3
β-strand	64-70	7	1
β-strand	73-86	14	1
β-strand	89-90	2	1
α-helix	91	1
α-helix	96-97	2
β-strand	108-110	3	3
β-strand	111	1	4
β-strand	117-124	8	3
β-strand	130-138	9	1
β-strand	146-148	3	3
β-strand	152-157	6	3
β-strand	164-173	10	3
α-helix	181-182	2
β-strand	186-194	9	1
β-strand	197-205	9	1
α-helix	207-209	3
β-strand	211	1	4
α-helix	213-216	4
β-strand	217-223	7	5
β-strand	229-235	7	5
β-strand	249-256	8	6
β-strand	266-269	4	6
β-strand	273-277	5	5
α-helix	278-279	2
β-strand	283-290	8	6
α-helix	299-300	2
β-strand	301-304	4	6

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-28	18
α-helix	54-56	3
α-helix	60-66	7
α-helix	68-85	18
α-helix	88-91	4
α-helix	95-97	3
α-helix	101-114	14
α-helix	136-167	32

Chain D: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	7
β-strand	8-14	7	7
β-strand	22-27	6	8
β-strand	37-40	4	7
β-strand	48-49	2	7
β-strand	52-57	6	8
α-helix	60-62	3
β-strand	64-70	7	7
β-strand	73-86	14	7
β-strand	89-90	2	7
β-strand	108-110	3	9
β-strand	111	1	10
β-strand	117-124	8	9
β-strand	130-138	9	7
α-helix	143	1
β-strand	144-145	2	7
β-strand	146-148	3	9
β-strand	152-158	7	9
β-strand	163-173	11	9
α-helix	181-182	2
β-strand	186-194	9	7
β-strand	197-205	9	7
α-helix	207-209	3
β-strand	211	1	10
α-helix	213-216	4
β-strand	217-223	7	11
β-strand	230-235	6	11
β-strand	249-256	8	12
β-strand	266-269	4	12
β-strand	273-276	4	11
β-strand	283-290	8	12
α-helix	299-300	2
β-strand	301-304	4	12

Chain E: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-52	8	15
β-strand	57-60	4	15
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	15
α-helix	100	1
α-helix	109-111	3
β-strand	112-115	4	15
β-strand	119-121	3	15
β-strand	122-123	2	14

Chain F: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	10-12	3	17
β-strand	18-23	6	16
β-strand	34-39	6	17
α-helix	44-45	2
β-strand	46-51	6	17
β-strand	58-60	3	17
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-98	7	17
α-helix	100-102	3
α-helix	103-106	4
β-strand	120-124	5	17

Chain G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	28C-28A	3
β-strand	29-35	7	19
β-strand	42-48	7	19
β-strand	53-56	4	19
β-strand	64-69	6	18
β-strand	74-79	6	18
α-helix	84-86	3
β-strand	88-95	8	19
α-helix	96	1
α-helix	105-107	3
β-strand	108-111	4	19
β-strand	115-119	5	19

Chain H: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-13	4	21
β-strand	18-24	7	20
β-strand	33-39	7	21
α-helix	44-45	2
β-strand	46-52	7	21
β-strand	55-60	6	21
α-helix	62-64	3
β-strand	68-73	6	20
β-strand	78-83	6	20
α-helix	88-90	3
β-strand	92-99	8	21
α-helix	107-109	3
β-strand	110-113	4	21
β-strand	117-122	6	21

2 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
Interleukin-23 subunit alpha	A, C	protein	189	Homo sapiens	Q9NPF7 (AlphaFold model)
Interleukin-12 subunit beta	B, D	protein	328	Homo sapiens	P29460 (AlphaFold model)
Nanobody 124C4	E, G	protein	125	Lama glama
Nanobody 37D5	F, J	protein	126	Lama glama
Nanobody 22E11	H, I	protein	123	Lama glama

Sequence of entity 1 (A, C), FASTA

>4GRW_1 Interleukin-23 subunit alpha (chains A, C)
MLGSRAVMLLLLLPWTAQGRAVPGGSSPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEG
DEETTNDVPHIQCGDGCDPQGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSP
VGQLHASLLGLSQLLQPEGHHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVF
AHGAATLSP

Sequence of entity 2 (B, D), FASTA

>4GRW_2 Interleukin-12 subunit beta (chains B, D)
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITW
TLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQ
KEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERV
RGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKN
LQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVIC
RKNASISVRAQDRYYSSSWSEWASVPCS

Sequence of entity 3 (E, G), FASTA

>4GRW_3 Nanobody 124C4 (chains E, G)
EVQLVESGGGLVQPGGSLRLSCAASGFTLDDYAIAWFRQAPGKEREGVSGIDSGDGSAYY
ADSVKGRFTISSDNAKNTVYLQMNSLRPEDTAVYYCARVRTGWGLNAPDYAMDYWGKGTL
VTVSS

Sequence of entity 4 (F, J), FASTA

>4GRW_4 Nanobody 37D5 (chains F, J)
EVQLVESGGGLVQPGGSLRLSCAASGFTLDYLAIGWFRQAPGKEREGVSCVSSSGQYTYY
ADSVKGRFTISRDNAESTVYLQMNSLKPEDTAVYYCATDPECYRVRGYYNGEYDYWGQGT
QVTVSS

Sequence of entity 5 (H, I), FASTA

>4GRW_5 Nanobody 22E11 (chains H, I)
EVQLVESGGGLVQAGGSLRLSCAASGRTFSWSAVGWFRQAPGKEREFVAAIRWSGGSPYY
ADSVKDRFTISRDNAKNTVYLQMNSLRPEDTAVYLCGETSLFPTSRGSHYDTWGQGTQVT
VSS

Primary citation

Neutralization of Human Interleukin 23 by Multivalent Nanobodies Explained by the Structure of Cytokine-Nanobody Complex. Desmyter, A., Spinelli, S., Boutton, C. et al. Front Immunol (2017) 8:884-884. DOI 10.3389/fimmu.2017.00884 · PubMed

Other PDB entries of the same protein (UniProt Q9NPF7 (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
5MXA 2.5 Å, Structure of unbound Interleukin-23
6UIB 2.74 Å, Crystal structure of IL23 bound to peptide 23-652
5MZV 2.8 Å, IL-23:IL-23R:Nb22E11 complex
3D87 2.9 Å, Crystal structure of Interleukin-23
3QWR 3.25 Å, Crystal structure of IL-23 in complex with an adnectin
5MJ4 3.4 Å, Interleukin-23 complex with an antagonistic alphabody, crystal form 2
6WDQ 3.4 Å, IL23/IL23R/IL12Rb1 signaling complex

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