7S2S: Nanobody

nanobody bound to Interleukin-2Rbeta. Determined by X-ray diffraction at 1.93 Å resolution. Released 30 Mar 2022.

Method: X-ray diffraction
Resolution: 1.93 Å
Organisms: Camelus bactrianus, Homo sapiens
Chains: 4
Atoms: 5,660
Mol. weight: 88.27 kDa
Released: 30 Mar 2022

Explore 7S2S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S2S contains 22 α-helices and 56 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: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	8
β-strand	11-12	2	9
β-strand	18-23	6	8
α-helix	26-31	6
β-strand	34-39	6	10
β-strand	46-51	6	10
β-strand	57-59	3	10
α-helix	61-63	3
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	87-89	3
β-strand	91-97	7	10
α-helix	98-99	2
α-helix	106-109	4
α-helix	112-114	3
β-strand	117-118	2	10
β-strand	122-124	3	10
β-strand	125-126	2	9

Chains B and D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	33-38	6	4
β-strand	43-49	7	4
β-strand	59-65	7	5
β-strand	72-75	4	5
β-strand	77-78	2	4
β-strand	83-89	7	4
β-strand	104-112	9	5
β-strand	115-124	10	5
α-helix	126-128	3
β-strand	130	1	4
α-helix	132-135	4
β-strand	136-143	8	6
β-strand	148-153	6	6
α-helix	159-162	4
β-strand	165-172	8	7
β-strand	183-186	4	7
β-strand	192-195	4	6
β-strand	203-212	10	7
α-helix	220-226	7
β-strand	227-230	4	7
α-helix	231-234	4

Chain C: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	11-13	3	2
β-strand	18-23	6	1
α-helix	26-31	6
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-97	7	3
α-helix	98-99	2
α-helix	106-109	4
α-helix	112-114	3
β-strand	117-118	2	3
β-strand	122-124	3	3
β-strand	125-127	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IL2Rb-binding nanobody	A, C	protein	154	Camelus bactrianus
Interleukin-2 receptor subunit beta	B, D	protein	216	Homo sapiens	P14784 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7S2S_1 IL2Rb-binding nanobody (chains A, C)
QVQLQESGGGSVQAGGSLRLSCAASSYTISSVCMGWFRQAPGKEREGVAGIAPDGSTGYG
DSVKGRFTISKDNAKNTLYLQMNSLKPEDTAMYYCAAASPGRCFLPRTALEPALYYNWGQ
GTQVTVSSGAPGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B, D), FASTA

>7S2S_2 Interleukin-2 receptor subunit beta (chains B, D)
AVNGTSQFTCFYNSRANISCVWSQDGALQDTSCQVHAWPDRRRWNQTCELLPVSQASWAC
NLILGAPDSQKLTTVDIVTLRVLCREGVRWRVMAIQDFKPFENLRLMAPISLQVVHVETH
RCNISWEISQASHYFERHLEFEARTLSPGHTWEEAPLLTLKQKQEWICLETLTPDTQYEF
QVRVKPLQGEFTTWSPWSQPLAFRTKPAALHHHHHH

Primary citation

Facile discovery of surrogate cytokine agonists. Yen, M., Ren, J., Liu, Q. et al. Cell (2022) 185:1414. DOI 10.1016/j.cell.2022.02.025 · PubMed

Other PDB entries of the same protein (UniProt P14784 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E8K 1.71 Å, Legionella Longbeachae LeSH (Llo2327) bound to the human interleukin-2 receptor beta…
2B5I 2.3 Å, cytokine receptor complex
5M5E 2.3 Å, Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor
4GS7 2.35 Å, Structure of the Interleukin-15 quaternary complex
9KMC 2.97 Å, Cryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with…
2ERJ 3.0 Å, Crystal structure of the heterotrimeric interleukin-2 receptor in complex with…
3QAZ 3.8 Å, IL-2 mutant D10 ternary complex

Browse structure collections

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