9CX9: SH3 domain of Src

Structure of SH3 domain of Src in complex with beta-arrestin 1. Determined by electron microscopy at 3.34 Å resolution. Released 13 Nov 2024.

Method: Electron microscopy
Resolution: 3.34 Å
Organisms: Mus musculus, Homo sapiens, Rattus norvegicus
Chains: 5
Atoms: 4,631
Mol. weight: 106.3 kDa
Released: 13 Nov 2024

Explore 9CX9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CX9 contains 14 α-helices and 58 β-strands across 5 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: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	10
β-strand	18-22	5	10
β-strand	26-28	3	11
β-strand	29	1	12
β-strand	34	1	12
α-helix	35-36	2
β-strand	37-43	7	10
β-strand	52-62	11	13
β-strand	76-87	12	13
α-helix	90	1
α-helix	94-97	4
α-helix	103-107	5
β-strand	112-117	6	10
α-helix	123-125	3
β-strand	127-129	3	14
β-strand	141	1	14
β-strand	142-151	10	13
α-helix	160-162	3
β-strand	163-168	6	13
β-strand	169-171	3	11
α-helix	180-182	3
β-strand	183-186	4	15
β-strand	198-203	6	15
β-strand	207-208	2	16
β-strand	214-221	8	15
β-strand	228-241	14	17
β-strand	247-257	11	17
β-strand	267-274	8	15
α-helix	278-281	4
β-strand	288-290	3	14
β-strand	300	1	14
α-helix	301-304	4
β-strand	317-329	13	17
β-strand	344-349	6	17
β-strand	350-351	2	16
α-helix	353-355	3

Chain B: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	102-103	2
α-helix	109-110	2
β-strand	112	1	18
β-strand	118-122	5	18
β-strand	129-133	5	18

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	13	1	2
β-strand	21-28	8	1
β-strand	35-42	8	3
β-strand	48-54	7	3
β-strand	61-62	2	3
β-strand	72-76	5	1
β-strand	81-86	6	1
α-helix	90-92	3
β-strand	96-103	8	3
β-strand	110-112	3	3
β-strand	117-118	2	3
β-strand	119	1	2

Chain L: 0 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	11-13	3	5
β-strand	20-26	7	4
β-strand	34-36	3	6
β-strand	37-38	2	7
β-strand	39	1	8
β-strand	46-47	2	7
β-strand	49-51	3	9
β-strand	54-55	2	9
β-strand	63-68	6	4
β-strand	71-76	6	4
β-strand	86-87	2	8
β-strand	89-91	3	6
β-strand	98-99	2	6
β-strand	103-104	2	8
β-strand	105-107	3	5

Chain V: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	357-360	4
β-strand	361-364	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody fragment Fab30, heavy chain	H	protein	237	Mus musculus
Antibody fragment Fab30, light chain	L	protein	215	Mus musculus
Vasopressin V2 receptor	V	protein	29	Homo sapiens	P30518 (AlphaFold model)
Beta-arrestin-1	A	protein	392	Rattus norvegicus	P29066 (AlphaFold model)
Proto-oncogene tyrosine-protein kinase Src	B	protein	85	Gallus gallus	P00523 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9CX9_1 Antibody fragment Fab30, heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHH

Sequence of entity 2 (L), FASTA

>9CX9_2 Antibody fragment Fab30, light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (V), FASTA

>9CX9_3 Vasopressin V2 receptor (chains V)
ARGRTPPSLGPQDESCTTASSSLAKDTSS

Sequence of entity 4 (A), FASTA

>9CX9_4 Beta-arrestin-1 (chains A)
GDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTVAF
RYGREDLDVLGLTFRKDLFVANVQSFPPAPCDKKPLTRLQERLIKKLGEHAYPFTFEIPP
NLPSSVTLQPGPEDTGKALGVDYEVKAFVAENLEEKIHKRNSVRLVIRKVQYAPERPGPQ
PTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADI
VLFNTAQYKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNLA
SSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPP
HREVPESETPVDTNLIELDTNDDDIVFEDFAR

Sequence of entity 5 (B), FASTA

>9CX9_5 Proto-oncogene tyrosine-protein kinase Src (chains B)
MGSSHHHHHHDYDIPTTENLYFQGHMVTTFVALYDYESCTETDLSFKKGERLQIVNNTEG
DWWLAHSLTTGQTGYIPSNYVAPSD

Primary citation

Mechanism of beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy. Pakharukova, N., Thomas, B.N., Bansia, H. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-69884-1 · PubMed

Other PDB entries of the same protein (UniProt P30518 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7DFC 2.49 Å, Crystal of Arrestin2-V2Rpp-3-Fab30 complex
9HAP 2.5 Å, Cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with…
9HB3 2.5 Å, cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with…
7DFA 2.54 Å, Crystal of Arrestin2-V2Rpp-4-Fab30 complex
4JQI 2.6 Å, Structure of active beta-arrestin1 bound to a G protein-coupled receptor phosphopeptide
7DW9 2.6 Å, Cryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein
9ZZO 2.6 Å, MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
7KH0 2.8 Å, Cryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs…
9WSV 2.8 Å, Cryo-EM structure of DAMGO-muOR-arrestin-1-Fab30 complex
9WSW 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-Gz-scFv16 complex
9WSX 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 complex

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