9CX3 | pdb_00009cx3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CX3

This is version 1.5 of the entry. See complete history

Literature

Mechanism of beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy.

Pakharukova, N.Thomas, B.N.Bansia, H.Li, L.Bassford, D.K.Abzalimov, R.R.Kim, J.Kahsai, A.W.Pani, B.Xiao, K.Ochakovski, R.Liu, S.Zhang, X.Ahn, S.des Georges, A.Lefkowitz, R.J.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69884-1
  • Primary Citation Related Structures: 
    9BT8, 9CX3, 9CX9

  • PubMed Abstract: 

    Beta-arrestins (βarrs) are key regulators and transducers of G-protein coupled receptor signaling; however, little is known of how βarrs communicate with their downstream effectors. Here, we delineate structural mechanisms underlying βarr-mediated signal transduction. Using cryo-electron microscopy, we elucidate how βarr1 recruits and activates the non-receptor tyrosine kinase Src, a well-established signaling partner of βarrs. βarr1 engages Src SH3 through two distinct sites, each employing a different recognition mechanism: a polyproline motif in the N-domain and a non-proline-based interaction in the central crest region. At both sites βarr1 interacts with the aromatic surface of SH3, disrupting the autoinhibited conformation of Src and directly triggering its allosteric activation. This structural evidence establishes βarr1 as an active regulatory protein rather than a passive scaffold and suggests a potentially general mechanism for βarr-mediated signaling across diverse effectors.


  • Organizational Affiliation
    • Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.

Macromolecule Content 

  • Total Structure Weight: 120 kDa 
  • Atom Count: 5,626 
  • Modeled Residue Count: 720 
  • Deposited Residue Count: 1,082 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 32124Lama glamaMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase SrcB [auth C]85Gallus gallusMutation(s): 1 
Gene Names: SRC
EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus)
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Go to UniProtKB:  P00523
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00523
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody fragment Fab30, heavy chainC [auth H]237Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Vasopressin V2 receptorD [auth V]29Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens)
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Go to UniProtKB:  P30518
PHAROS:  P30518
GTEx:  ENSG00000126895 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30518
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-arrestin-1E [auth B]392Rattus norvegicusMutation(s): 8 
Gene Names: Arrb1
UniProt
Find proteins for P29066 (Rattus norvegicus)
Explore P29066 
Go to UniProtKB:  P29066
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29066
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody fragment Fab30, light chainF [auth L]215Mus musculusMutation(s): 0 

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
D [auth V]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
D [auth V]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487-000
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL016037-50
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133598
Human Frontier Science Program (HFSP)FranceLT000174/2018
European Molecular Biology Organization (EMBO)European UnionALTF 1071-2017

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection
  • Version 1.2: 2025-10-22
    Changes: Data collection, Database references
  • Version 1.3: 2025-10-29
    Changes: Data collection, Database references
  • Version 1.4: 2026-03-04
    Changes: Data collection, Database references
  • Version 1.5: 2026-04-08
    Changes: Data collection, Database references