7YQE: Human SRC regulatory domains

Structure of human SRC regulatory domains in complex with the C-terminal PRRP motifs of GPR54. Determined by X-ray diffraction at 3.5 Å resolution. Released 16 Aug 2023.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,736
Mol. weight: 42.81 kDa
Released: 16 Aug 2023

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

Secondary structure: helices and β-sheets

7YQE contains 8 α-helices and 32 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	89-91	3	1
β-strand	95	1	2
β-strand	102	1	1
β-strand	105	1	2
β-strand	110-115	6	1
β-strand	121-126	6	1
β-strand	132-136	5	1
α-helix	137-139	3
β-strand	140-142	3	1
β-strand	152-154	3	3
α-helix	158-165	8
β-strand	175-179	5	3
β-strand	187-195	9	3
β-strand	199-207	9	3
β-strand	208-209	2	4
α-helix	210	1
β-strand	215-218	4	4
β-strand	221-223	3	4
α-helix	226-233	8
β-strand	247	1	3
α-helix	337-343	7

Chain B: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	89-91	3	5
β-strand	95	1	6
β-strand	102	1	5
β-strand	105	1	6
β-strand	110-115	6	5
β-strand	121-126	6	5
β-strand	132-136	5	5
α-helix	137-139	3
β-strand	140-142	3	5
β-strand	152	1	7
α-helix	158-165	8
β-strand	175-179	5	7
β-strand	187-195	9	7
β-strand	199-207	9	7
β-strand	208-209	2	8
β-strand	215-218	4	8
β-strand	221-223	3	8
α-helix	226-233	8
β-strand	247	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor	A, B	protein	188	Homo sapiens	P12931 (AlphaFold model), Q969F8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7YQE_1 Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor (chains A, B)
GVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSD
SIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKH
YKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVAFRRVSPSAPRRPRRPR
RPGPSDPA

Primary citation

Kisspeptin-10 binding to Gpr54 in osteoclasts prevents bone loss by activating Dusp18-mediated dephosphorylation of Src. Li, Z., Yang, X., Fu, R. et al. Nat Commun (2024) 15:1300-1300. DOI 10.1038/s41467-024-44852-9 · PubMed

Other PDB entries of the same protein (UniProt P12931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OFX 1.45 Å, Crystal structure of c-Src SH3 domain in H32 space group mediated by nickel
1FMK 1.5 Å, Crystal structure of human tyrosine-protein kinase C-src
1O43 1.5 Å, Crystal structure of SH2 in complex with RU82129.
1O4A 1.5 Å, Crystal structure of SH2 in complex with RU82197.
1O4R 1.5 Å, Crystal structure of SH2 in complex with RU78783.
2SRC 1.5 Å, Crystal structure of human tyrosine-protein kinase C-src, in complex with AMP-pnp
6C4S 1.5 Å, Human cSrc SH3 Domain in complex with Choline Kinase fragment 60-69
7NG7 1.5 Å, Src kinase bound to eCF506 trapped in inactive conformation
8VCF 1.5 Å, Crystal structure of Superbinder Src SH2 domain with Cysteine to Serine mutations
1O48 1.55 Å, Crystal structure of SH2 in complex with RU85053.
1O4G 1.55 Å, Crystal structure of SH2 in complex with DPI59.
1O4K 1.57 Å, Crystal structure of SH2 in complex with pasbn.

Browse structure collections

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