9BT8: Src

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

Method: Electron microscopy
Resolution: 3.34 Å
Organisms: Gallus gallus, Bacteriophage sp., Homo sapiens
Chains: 6
Atoms: 5,712
Mol. weight: 164.77 kDa
Released: 13 Nov 2024

Explore 9BT8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BT8 contains 17 α-helices and 67 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: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-12	3	9
β-strand	17-24	8	8
α-helix	33	1
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	68-72	5	8
β-strand	77-83	7	8
α-helix	87-89	3
β-strand	91-97	7	9
β-strand	108-112	5	9

Chain B: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	7
β-strand	18-22	5	7
β-strand	26-28	3	10
β-strand	29	1	11
β-strand	34	1	11
β-strand	37-43	7	7
β-strand	52-62	11	12
β-strand	74-82	9	12
α-helix	99-108	10
β-strand	112-117	6	7
β-strand	127-129	3	12
α-helix	130-131	2
α-helix	139	1
β-strand	141-151	11	12
β-strand	163-168	6	12
β-strand	169-171	3	10
α-helix	180-182	3
β-strand	183-188	6	13
α-helix	196	1
β-strand	197-202	6	13
β-strand	207-208	2	14
β-strand	214-222	9	13
β-strand	228-241	14	15
β-strand	247-258	12	15
β-strand	262	1	15
β-strand	266-274	9	13
β-strand	288-290	3	12
β-strand	300	1	12
α-helix	301-305	5
β-strand	317-329	13	15
β-strand	342-349	8	15
β-strand	350-351	2	14
α-helix	353-355	3

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	87-88	2	1
α-helix	89	1
β-strand	92	1	2
β-strand	102	1	2
β-strand	107	1	1
β-strand	108-110	3	3
β-strand	118-123	6	3
β-strand	129-133	5	3
α-helix	134-136	3
β-strand	137-138	2	1

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	4
β-strand	14	1	5
β-strand	21-28	8	4
α-helix	32-34	3
β-strand	35-42	8	6
β-strand	48-55	8	6
β-strand	60-63	4	6
β-strand	71-76	6	4
β-strand	81-86	6	4
α-helix	91-93	3
β-strand	95-103	9	6
β-strand	112-119	8	6
β-strand	120	1	5

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	16
β-strand	11-13	3	17
β-strand	20-26	7	16
β-strand	34-39	6	17
β-strand	46-49	4	17
α-helix	54	1
β-strand	55	1	17
α-helix	56	1
β-strand	63-67	5	16
β-strand	71-76	6	16
β-strand	86-91	6	17
β-strand	98-99	2	17
β-strand	103-106	4	17

Chain V: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	358-360	3
β-strand	361-364	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase Src	C	protein	477	Gallus gallus	P00523 (AlphaFold model)
Antibody fragment Fab30, heavy chain	H	protein	237	Bacteriophage sp.
Vasopressin V2 receptor	V	protein	29	Homo sapiens	P30518 (AlphaFold model)
Nanobody 32	A	protein	124	Lama glama
Beta-arrestin-1	B	protein	392	Rattus norvegicus	P29066 (AlphaFold model)
Antibody fragment Fab30, light chain	L	protein	215	Bacteriophage sp.

Sequence of entity 1 (C), FASTA

>9BT8_1 Proto-oncogene tyrosine-protein kinase Src (chains C)
MGSSHHHHHHDYDIPTTENLYFQGHMVTTFVALYDYESCTETDLSFKKGERLQIVNNTEG
DWWLAHSLTTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNPENPRGTFLVRE
SETTKGAYSLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADG
LSHRLTNVSPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGSFGEVWMGTWNGTTRVAIKT
LKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGEMGK
YLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVSKVADFGLARLIEDNEY
TARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVE
RGYRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQPGENL

Sequence of entity 2 (H), FASTA

>9BT8_2 Antibody fragment Fab30, heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHH

Sequence of entity 3 (V), FASTA

>9BT8_3 Vasopressin V2 receptor (chains V)
ARGRTPPSLGPQDESCTTASSSLAKDTSS

Sequence of entity 4 (A), FASTA

>9BT8_4 Nanobody 32 (chains A)
QVQLQESGGGLVQAGGSLRLSCVVSGFFFDTVTMAWYRRAPGKHRELVASATAGGTTTYA
DSVKDRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNTFVRSLSWGQGTQVTVSSHHHHHH
EPEA

Sequence of entity 5 (B), FASTA

>9BT8_5 Beta-arrestin-1 (chains B)
GDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTVAF
RYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEICP
NLPSSVTLQPGPEDTGKALGVDYEVKAFVAENLEEKIHKRNSVRLVIRKVQYAPERPGPQ
PTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADI
VLFNTAQYKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNLA
SSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPP
HREVPESETPVDTNLIELDTNDDDIVFEDFAR

Sequence of entity 6 (L), FASTA

>9BT8_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…

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