9CX3: SH3 domain of Src

Structure of SH3 domain of Src in complex with beta-arrestin 1. Determined by electron microscopy at 3.47 Å resolution. Released 13 Nov 2024.

Method: Electron microscopy
Resolution: 3.47 Å
Organisms: Lama glama, Gallus gallus, Mus musculus
Chains: 6
Atoms: 5,626
Mol. weight: 120 kDa
Released: 13 Nov 2024

Explore 9CX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CX3 contains 14 α-helices and 70 β-strands across 6 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: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	34-39	6	2
α-helix	44	1
β-strand	45-51	7	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-97	7	2
β-strand	108-112	5	2

Chain B: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	8
β-strand	18-22	5	8
β-strand	26-28	3	9
β-strand	29	1	10
β-strand	34	1	10
α-helix	35-36	2
β-strand	37-43	7	8
α-helix	45-48	4
β-strand	53-62	10	11
β-strand	74-82	9	11
α-helix	99-108	10
β-strand	113-117	5	8
β-strand	127-128	2	12
α-helix	129-132	4
β-strand	141	1	12
β-strand	142-150	9	11
α-helix	160-162	3
β-strand	164-168	5	11
β-strand	169-171	3	9
β-strand	183-188	6	13
β-strand	197-202	6	13
β-strand	207-208	2	14
α-helix	209	1
β-strand	214-221	8	13
β-strand	228	1	15
β-strand	230-241	12	16
β-strand	248-258	11	16
β-strand	262	1	15
β-strand	267-274	8	13
β-strand	289-290	2	12
α-helix	291-292	2
β-strand	300	1	12
α-helix	301-303	3
β-strand	317-328	12	16
β-strand	342-349	8	16
β-strand	350-351	2	14
α-helix	353-355	3

Chain C: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	87	1	3
β-strand	91-92	2	4
β-strand	99	1	5
β-strand	102-103	2	4
β-strand	109	1	5
β-strand	119-122	4	5
β-strand	129-132	4	5
α-helix	134-136	3
β-strand	138	1	3

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	6
β-strand	21-22	2	6
β-strand	24-26	3	6
β-strand	35-42	8	7
β-strand	48-54	7	7
β-strand	61-63	3	7
α-helix	65-67	3
β-strand	71-76	6	6
β-strand	81-86	6	6
α-helix	91-93	3
β-strand	96-103	8	7
β-strand	113	1	7
β-strand	117-118	2	7

Chain L: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	17
β-strand	11-12	2	18
β-strand	20-23	4	19
β-strand	25	1	17
β-strand	34-39	6	20
β-strand	46-50	5	20
β-strand	54-55	2	20
β-strand	65-68	4	19
β-strand	71-76	6	19
β-strand	86-91	6	20
β-strand	98-99	2	20
β-strand	103	1	20
β-strand	104-105	2	18

Chain V: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	361-364	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody 32	A	protein	124	Lama glama
Proto-oncogene tyrosine-protein kinase Src	C	protein	85	Gallus gallus	P00523 (AlphaFold model)
Antibody fragment Fab30, heavy chain	H	protein	237	Mus musculus
Vasopressin V2 receptor	V	protein	29	Homo sapiens	P30518 (AlphaFold model)
Beta-arrestin-1	B	protein	392	Rattus norvegicus	P29066 (AlphaFold model)
Antibody fragment Fab30, light chain	L	protein	215	Mus musculus

Sequence of entity 1 (A), FASTA

>9CX3_1 Nanobody 32 (chains A)
QVQLQESGGGLVQAGGSLRLSCVVSGFFFDTVTMAWYRRAPGKHRELVASATAGGTTTYA
DSVKDRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNTFVRSLSWGQGTQVTVSSHHHHHH
EPEA

Sequence of entity 2 (C), FASTA

>9CX3_2 Proto-oncogene tyrosine-protein kinase Src (chains C)
MGSSHHHHHHDYDIPTTENLYFQGHMVTTFVALYDYESCTETDLSFKKGERLQIVNNTEG
DWWLAHSLTTGQTGYIPSNYVAPSD

Sequence of entity 3 (H), FASTA

>9CX3_3 Antibody fragment Fab30, heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHH

Sequence of entity 4 (V), FASTA

>9CX3_4 Vasopressin V2 receptor (chains V)
ARGRTPPSLGPQDESCTTASSSLAKDTSS

Sequence of entity 5 (B), FASTA

>9CX3_5 Beta-arrestin-1 (chains B)
GDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTVAF
RYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEICP
NLPSSVTLQPGPEDTGKALGVDYEVKAFVAENLEEKIHKRNSVRLVIRKVQYAPERPGPQ
PTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADI
VLFNTAQYKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNLA
SSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPP
HREVPESETPVDTNLIELDTNDDDIVFEDFAR

Sequence of entity 6 (L), FASTA

>9CX3_6 Antibody fragment Fab30, light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 P00523 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XVM 0.9 Å, Crystal structure of c-Src SH3 domain without ATCUN motif: monomer 2
7A31 0.94 Å, Crystal structure of the c-Src SH3 domain mutant S94A-T98D-V111L-N113S-T114S at pH 4.5
5OAV 0.95 Å, High resolution crystal structure of the c-Src-SH3 domain mutant E93V in complex with…
7A33 0.96 Å, Crystal structure of the c-Src SH3 domain mutant S94A-T98D-V111L-N113S-T114S at pH 3.0
4RTZ 0.98 Å, Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12
4HVU 0.98 Å, Crystal structure of the T98D c-Src-SH3 domain mutant in complex with the high affinity…
4HVW 0.98 Å, Crystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity…
4OMO 1.04 Å, Crystal structure of the c-Src tyrosine kinase SH3 domain mutant Q128E
6XX4 1.05 Å, Crystal structure of the c-Src SH3 domain H122R-Q128E mutant in complex with Ni(II) at…
4HVV 1.1 Å, Crystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity…
7A32 1.15 Å, Crystal structure of the c-Src SH3 domain mutant S94A-T98D-V111L-N113S-T114S at pH 7.0
5ECA 1.16 Å, Crystal structure of a chimeric c-Src-SH3 domain with the sequence of the RT-loop from…

Browse structure collections

About this viewer

MolViewer shows 9CX3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.