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- PDB-8go8: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: PDB / ID: 8go8
TitleStructure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1
Components
  • Beta-arrestin-1
  • C5a anaphylatoxin chemotactic receptor 1
  • Fab30 heavy chain
  • Fab30 light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / presynapse organization / sensory perception of touch / complement component C5a signaling pathway / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / presynapse organization / sensory perception of touch / complement component C5a signaling pathway / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid binding / Lysosome Vesicle Biogenesis / complement component C5a receptor activity / response to peptidoglycan / Ub-specific processing proteases / regulation of inositol trisphosphate biosynthetic process / AP-2 adaptor complex binding / angiotensin receptor binding / MAP2K and MAPK activation / Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-cargo adaptor activity / negative regulation of interleukin-8 production / sensory perception of chemical stimulus / desensitization of G protein-coupled receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / mitogen-activated protein kinase kinase binding / positive regulation of neutrophil chemotaxis / Thrombin signalling through proteinase activated receptors (PARs) / sensory perception / clathrin binding / stress fiber assembly / response to morphine / positive regulation of macrophage chemotaxis / positive regulation of Rho protein signal transduction / negative regulation of interleukin-6 production / pseudopodium / amyloid-beta clearance / positive regulation of receptor internalization / phototransduction / negative regulation of Notch signaling pathway / positive regulation of vascular endothelial growth factor production / cysteine-type endopeptidase inhibitor activity / cellular defense response / insulin-like growth factor receptor binding / neutrophil chemotaxis / clathrin-coated pit / negative regulation of protein ubiquitination / astrocyte activation / Regulation of Complement cascade / secretory granule membrane / nuclear estrogen receptor binding / positive regulation of epithelial cell proliferation / Peptide ligand-binding receptors / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of protein ubiquitination / GTPase activator activity / phosphoprotein binding / microglial cell activation / negative regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / G protein-coupled receptor activity / cognition / chemotaxis / endocytosis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of angiogenesis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / apical part of cell / protein transport / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / regulation of apoptotic process / G alpha (i) signalling events / molecular adaptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / basolateral plasma membrane / ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / postsynaptic membrane / endosome / postsynaptic density / defense response to Gram-positive bacterium / nuclear body / immune response / protein ubiquitination / G protein-coupled receptor signaling pathway / response to xenobiotic stimulus
Similarity search - Function
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / 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 / G-protein coupled receptors family 1 signature. / Immunoglobulin E-set / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
C5a anaphylatoxin chemotactic receptor 1 / Beta-arrestin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsMaharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Citation
Journal: Mol Cell / Year: 2023
Title: Structural snapshots uncover a key phosphorylation motif in GPCRs driving β-arrestin activation.
Authors: Jagannath Maharana / Parishmita Sarma / Manish K Yadav / Sayantan Saha / Vinay Singh / Shirsha Saha / Mohamed Chami / Ramanuj Banerjee / Arun K Shukla /
Abstract: Agonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent ...Agonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent phosphorylation patterns impart converging active conformation on βarrs leading to broadly conserved functional responses such as desensitization, endocytosis, and signaling. Here, we present multiple cryo-EM structures of activated βarrs in complex with distinct phosphorylation patterns derived from the carboxyl terminus of different GPCRs. These structures help identify a P-X-P-P type phosphorylation motif in GPCRs that interacts with a spatially organized K-K-R-R-K-K sequence in the N-domain of βarrs. Sequence analysis of the human GPCRome reveals the presence of this phosphorylation pattern in a large number of receptors, and its contribution in βarr activation is demonstrated by targeted mutagenesis experiments combined with an intrabody-based conformational sensor. Taken together, our findings provide important structural insights into the ability of distinct GPCRs to activate βarrs through a significantly conserved mechanism.
#1: Journal: Mol.Cell / Year: 2023
Title: Structure of beta-arrestin in complex with a phosphopeptide
Authors: Maharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K.
History
DepositionAug 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
V: C5a anaphylatoxin chemotactic receptor 1
B: Beta-arrestin-1
U: C5a anaphylatoxin chemotactic receptor 1
H: Fab30 heavy chain
I: Fab30 heavy chain
L: Fab30 light chain
M: Fab30 light chain


Theoretical massNumber of molelcules
Total (without water)197,4698
Polymers197,4698
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Beta-arrestin-1 / Arrestin beta-1


Mass: 47088.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29066
#2: Protein/peptide C5a anaphylatoxin chemotactic receptor 1 / C5a anaphylatoxin chemotactic receptor / C5a-R / C5aR


Mass: 2698.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21730
#3: Antibody Fab30 heavy chain


Mass: 25512.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab30 light chain


Mass: 23435.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Peptide bound beta-arrestin1 in complex with Fab30COMPLEXall0MULTIPLE SOURCES
2beta-arrestin1COMPLEX#11RECOMBINANT
3C5a anaphylatoxin chemotactic receptor 1COMPLEX#21SYNTHETIC
4Fab30COMPLEX#3-#41RECOMBINANT
Molecular weightValue: 0.19 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Rattus norvegicus (Norway rat)10116
23Homo sapiens (human)9606
34Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2300 mMSodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K / Details: Blotted for 3 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6212
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
12cryoSPARC3.3.1classification
13cryoSPARC3.3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 4304237
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84655 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 4JQI

4jqi


Accession code: 4JQI / Source name: PDB / Type: experimental model

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