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- PDB-9cx3: Structure of SH3 domain of Src in complex with beta-arrestin 1 -

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Basic information

Entry
Database: PDB / ID: 9cx3
TitleStructure of SH3 domain of Src in complex with beta-arrestin 1
Components
  • (Antibody fragment Fab30, ...) x 2
  • Beta-arrestin-1
  • Nanobody 32
  • Proto-oncogene tyrosine-protein kinase Src
  • Vasopressin V2 receptor
KeywordsSIGNALING PROTEIN / GPCR signaling / arrestin / Src / SH3 / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V2 vasopressin receptor binding / regulation of inositol trisphosphate biosynthetic process / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / sensory perception of touch / G alpha (s) signalling events / Vasopressin-like receptors ...V2 vasopressin receptor binding / regulation of inositol trisphosphate biosynthetic process / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / sensory perception of touch / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / Lysosome Vesicle Biogenesis / angiotensin receptor binding / Golgi Associated Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / MAP2K and MAPK activation / hemostasis / Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / telencephalon development / MAP2K and MAPK activation / Cargo recognition for clathrin-mediated endocytosis / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / clathrin adaptor activity / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / negative regulation of interleukin-8 production / Clathrin-mediated endocytosis / regulation of G protein-coupled receptor signaling pathway / connexin binding / G protein-coupled receptor internalization / arrestin family protein binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Thrombin signalling through proteinase activated receptors (PARs) / response to morphine / mitogen-activated protein kinase kinase binding / clathrin binding / positive regulation of Rho protein signal transduction / stress fiber assembly / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of systemic arterial blood pressure / pseudopodium / negative regulation of interleukin-6 production / positive regulation of intracellular signal transduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of receptor internalization / endocytic vesicle / immune system process / negative regulation of Notch signaling pathway / phototransduction / progesterone receptor signaling pathway / cellular response to hormone stimulus / activation of adenylate cyclase activity / clathrin-coated pit / insulin-like growth factor receptor binding / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / response to cytokine / GTPase activator activity / positive regulation of protein ubiquitination / nuclear estrogen receptor binding / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity
Similarity search - Function
Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src / Beta-arrestin-1 / Vasopressin V2 receptor
Similarity search - Component
Biological speciesLama glama (llama)
Gallus gallus (chicken)
Mus musculus (house mouse)
Rattus norvegicus (Norway rat)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsPakharukova, N. / Bansia, H. / des Georges, A. / Lefkowitz, R.J.
Funding support United States, France, European Union, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL016037-50 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133598 United States
Human Frontier Science Program (HFSP)LT000174/2018 France
European Molecular Biology Organization (EMBO)ALTF 1071-2017European Union
CitationJournal: bioRxiv / Year: 2024
Title: Beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy.
Authors: Natalia Pakharukova / Brittany N Thomas / Harsh Bansia / Linus Li / Rinat R Abzalimov / Jihee Kim / Alem W Kahsai / Biswaranjan Pani / Dana K Bassford / Shibo Liu / Xingdong Zhang / Amedee ...Authors: Natalia Pakharukova / Brittany N Thomas / Harsh Bansia / Linus Li / Rinat R Abzalimov / Jihee Kim / Alem W Kahsai / Biswaranjan Pani / Dana K Bassford / Shibo Liu / Xingdong Zhang / Amedee des Georges / Robert J Lefkowitz /
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 ...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.
History
DepositionJul 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody 32
C: Proto-oncogene tyrosine-protein kinase Src
H: Antibody fragment Fab30, heavy chain
V: Vasopressin V2 receptor
B: Beta-arrestin-1
L: Antibody fragment Fab30, light chain


Theoretical massNumber of molelcules
Total (without water)120,0016
Polymers120,0016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules CB

#2: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 9756.567 Da / Num. of mol.: 1 / Mutation: R95C
Source method: isolated from a genetically manipulated source
Details: SH3 domain of Src / Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#5: Protein Beta-arrestin-1


Mass: 44081.160 Da / Num. of mol.: 1
Mutation: C59V, P120C, C125S, C140L, C150V, C242V, C251V, C269S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P29066

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Protein/peptide , 1 types, 1 molecules V

#4: Protein/peptide Vasopressin V2 receptor


Mass: 3550.936 Da / Num. of mol.: 1 / Fragment: UNP residues 343-371 / Source method: obtained synthetically
Details: Synthetic phosphopeptide mimicking the C-tail of vasopressin 2 receptor
Source: (synth.) Homo sapiens (human) / References: UniProt: P30518

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Antibody , 3 types, 3 molecules AHL

#1: Antibody Nanobody 32


Mass: 13665.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody Antibody fragment Fab30, heavy chain


Mass: 25512.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#6: Antibody Antibody fragment Fab30, light chain


Mass: 23435.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Beta-arrestin 1 bound to a G protein-coupled receptor phosphopeptide, nanobody 32 and antibody fragment Fab30 in complex with SH3 domain of Src
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4.4.1CTF correction
7Coot0.9.8.3model fitting
8ISOLDEmodel fitting
10PHENIX1.20.1-4487-000model refinement
14cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200270 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDChain-ID
16ni2

6ni2

6ni21
26ni2

6ni2

B6ni21B
36ni2

6ni2

V6ni21V
46ni2

6ni2

L6ni21L
56ni2

6ni2

H6ni21H
62ptk

2ptk

C2ptk2C
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0085794
ELECTRON MICROSCOPYf_angle_d1.0867874
ELECTRON MICROSCOPYf_dihedral_angle_d6.502809
ELECTRON MICROSCOPYf_chiral_restr0.041891
ELECTRON MICROSCOPYf_plane_restr0.005994

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