7S2R: Nanobody

nanobody bound to IL-2Rg. Determined by X-ray diffraction at 2.49 Å resolution. Released 30 Mar 2022.

Method: X-ray diffraction
Resolution: 2.49 Å
Organisms: Homo sapiens, Camelus bactrianus
Chains: 2
Atoms: 2,841
Mol. weight: 45.16 kDa
Ligands: NAG
Released: 30 Mar 2022

Explore 7S2R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S2R contains 11 α-helices and 27 β-strands across 2 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, 16 β-strands

Element	Residues	Length	Sheet
α-helix	53-60	8
β-strand	61-65	5	1
β-strand	69-73	5	1
β-strand	86-91	6	2
α-helix	99	1
β-strand	100-101	2	2
α-helix	102	1
β-strand	105-107	3	1
β-strand	112-118	7	1
α-helix	119-121	3
β-strand	128-134	7	2
β-strand	137-146	10	2
α-helix	148-150	3
β-strand	152-153	2	1
α-helix	154-157	4
β-strand	158-166	9	3
β-strand	169-175	7	3
α-helix	180-182	3
β-strand	184-191	8	4
β-strand	198-202	5	4
β-strand	207-209	3	3
β-strand	219-226	8	4
α-helix	237-243	7
β-strand	244-246	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	5
β-strand	10-13	4	6
β-strand	18-26	9	5
β-strand	33-39	7	6
β-strand	45-52	8	6
β-strand	61-63	3	6
β-strand	71-76	6	5
β-strand	81-86	6	5
α-helix	91-93	3
β-strand	95-102	8	6
α-helix	115-116	2
α-helix	117-119	3
β-strand	122-123	2	6
β-strand	127-132	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytokine receptor common subunit gamma	A	protein	209	Homo sapiens	P31785 (AlphaFold model)
nanobody gamma-nb6	B	protein	159	Camelus bactrianus

Sequence of entity 1 (A), FASTA

>7S2R_1 Cytokine receptor common subunit gamma (chains A)
ADPLPLPEVQCFVFNVEYMNCTWNSSSEPQPTNLTLHYWYKNSDNDKVQKCSHYLFSEEI
TSGCQLQKKEIHLYQTFVVQLQDPREPRRQATQMLKLQNLVIPWAPENLTLHKLSESQLE
LNWNNRFLNHCLEHLVQYRTDWDHSWTEQSVDYRHKFSLPSVDGQKRYTFRVRSRFNPLC
GSAQHWSEWSHPIHWGSNTSKENHHHHHH

Sequence of entity 2 (B), FASTA

>7S2R_2 nanobody gamma-nb6 (chains B)
QVQLQESGGGSVQAGGSLRLSCAASGYTYRDYYMGWFRQAPGREREGVASIYTRGSREGS
TRYSSSVEGRFTITLDTAKNTLYLQMNSLKPEDTAMYYCAADDRTWLPRVQLGGPRENEY
NYWGQGTQVTVSSGAPGSGLNDIFEAQKIEWHEHHHHHH

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 (GOL, SO4) are not listed.

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 P31785 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E2T 2.28 Å, Structure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg
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
9JQT 2.7 Å, Structure of interleukin receptor common gamma chain (IL2Rgamma/CD132) in complex with 2D4
8ENT 2.83 Å, Interleukin-21 signaling complex with IL-21R and IL-2Rg
3BPL 2.93 Å, Crystal structure of the IL4-IL4R-Common Gamma ternary 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…
6OEL 3.1 Å, Engineered Fab bound to IL-4 receptor
3QB7 3.25 Å, Interleukin-4 mutant RGA bound to cytokine receptor common gamma
8EPA 3.4 Å, Structure of interleukin receptor common gamma chain (IL2Rgamma) in complex with two…

Browse structure collections

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