› 9cx9

Electron Microscopy
3.34Å resolution

Structure of SH3 domain of Src in complex with beta-arrestin 1

Released:
DOI: 10.2210/pdb9cx9/pdb
PDB entry 9cx9 coloured by chain, front view.
PDB entry 9cx9 coloured by chain, side view.
PDB entry 9cx9 coloured by chain, top view.
Source organisms:
Primary publication:
Beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy.
Pakharukova N, Thomas BN, Bansia H, Li L, Abzalimov RR, Kim J, Kahsai AW, Pani B, Bassford DK, Liu S, Zhang X, des Georges A, Lefkowitz RJ
bioRxiv (2024)
PMID: 39131402
Related structures: EMD-45982

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-281429 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Antibody fragment Fab30, heavy chain Chain: H
Molecule details ›
Chain: H
Length: 237 amino acids
Theoretical weight: 25.51 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Antibody fragment Fab30, light chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.44 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Vasopressin V2 receptor Chain: V
Molecule details ›
Chain: V
Length: 29 amino acids
Theoretical weight: 3.55 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P30518 (Residues: 343-371; Coverage: 8%)
Gene names: ADHR, AVPR2, DIR, DIR3, V2R
Beta-arrestin-1 Chain: A
Molecule details ›
Chain: A
Length: 392 amino acids
Theoretical weight: 44.05 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P29066 (Residues: 2-393; Coverage: 94%)
Gene name: Arrb1
Sequence domains:
Proto-oncogene tyrosine-protein kinase Src Chain: B
Molecule details ›
Chain: B
Length: 85 amino acids
Theoretical weight: 9.76 KDa
Source organism: Gallus gallus
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P00523 (Residues: 83-141; Coverage: 11%)
Gene name: SRC
Sequence domains: SH3 domain

Ligands and Environments

No bound ligands
2 modified residues:
Ligand TPO 3 x TPO
Ligand SEP 5 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.34Å
Relevant EMDB volumes: EMD-45982
Expression systems:
  • Escherichia coli
  • Not provided
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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