9CX3

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


This is version 1.1 of the entry. See complete history


Literature

Beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy.

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

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.07.31.605623
  • Primary Citation of 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 use cryo-electron microscopy to elucidate how βarr1 recruits and activates non-receptor tyrosine kinase Src. βarr1 binds Src SH3 domain via two distinct sites: a polyproline site in the N-domain and a non-proline site in the central crest region. At both sites βarr1 interacts with the aromatic surface of SH3 which is critical for Src autoinhibition, suggesting that βarr1 activates Src by SH3 domain displacement. Binding of SH3 to the central crest region induces structural rearrangements in the β-strand V, finger, and middle loops of βarr1 and interferes with βarr1 coupling to the receptor core potentially impacting receptor desensitization and downstream signaling.


  • Organizational Affiliation

    Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA.


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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UniProt GroupP00523
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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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PHAROS:  P30518
GTEx:  ENSG00000126895 
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UniProt GroupP30518
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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)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody fragment Fab30, light chainF [auth L]215Mus musculusMutation(s): 0 
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  • Reference Sequence
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