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- PDB-8gp3: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: PDB / ID: 8gp3
TitleStructure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4
Components
  • Beta-arrestin-1
  • C-X-C chemokine receptor type 4
  • Fab30 Heavy Chain
  • Fab30 Light Chain
KeywordsSIGNALING PROTEIN / GPCR / Arrestin
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 / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / regulation of viral process / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / positive regulation of vascular wound healing ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / regulation of viral process / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / positive regulation of vascular wound healing / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / positive regulation of macrophage migration inhibitory factor signaling pathway / angiotensin receptor binding / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / telencephalon cell migration / C-X-C chemokine receptor activity / response to tacrolimus / Specification of primordial germ cells / Lysosome Vesicle Biogenesis / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / AP-2 adaptor complex binding / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / positive regulation of smooth muscle cell apoptotic process / endothelial tube morphogenesis / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / C-C chemokine receptor activity / endothelial cell differentiation / Clathrin-mediated endocytosis / clathrin adaptor activity / Signaling by ROBO receptors / regulation of chemotaxis / : / C-C chemokine binding / positive regulation of dendrite extension / positive regulation of chemotaxis / Formation of definitive endoderm / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / Chemokine receptors bind chemokines / Thrombin signalling through proteinase activated receptors (PARs) / anchoring junction / dendritic cell chemotaxis / response to morphine / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / positive regulation of oligodendrocyte differentiation / small molecule binding / stress fiber assembly / negative regulation of Notch signaling pathway / epithelial cell development / cell leading edge / cellular response to cytokine stimulus / positive regulation of receptor internalization / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / regulation of calcium ion transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / phototransduction / detection of mechanical stimulus involved in sensory perception of pain / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / cardiac muscle contraction / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / GTPase activator activity / neurogenesis / negative regulation of protein phosphorylation / cell chemotaxis / positive regulation of protein ubiquitination / ubiquitin binding / response to activity / nuclear estrogen receptor binding / G protein-coupled receptor binding / G protein-coupled receptor activity / phosphoprotein binding / calcium-mediated signaling / neuron migration / brain development / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / endocytosis / late endosome
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / 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 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / 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 / Chemokine receptor family / Arrestin-like, C-terminal / : / 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) / Immunoglobulin E-set
Similarity search - Domain/homology
Beta-arrestin-1 / C-X-C chemokine receptor type 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 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 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-arrestin-1
V: C-X-C chemokine receptor type 4
B: Beta-arrestin-1
U: C-X-C chemokine receptor type 4
H: Fab30 Heavy Chain
I: Fab30 Heavy Chain
L: Fab30 Light Chain
M: Fab30 Light Chain


Theoretical massNumber of molelcules
Total (without water)196,8338
Polymers196,8338
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14160 Å2
ΔGint-125 kcal/mol
Surface area75870 Å2

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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 C-X-C chemokine receptor type 4 / CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain ...CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain receptor / LESTR / Lipopolysaccharide-associated protein 3 / LAP-3 / LPS-associated protein 3 / NPYRL / Stromal cell-derived factor 1 receptor / SDF-1 receptor


Mass: 2380.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61073
#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

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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
1Peptide5 bound beta-arrestin1 in complex with Fab30COMPLEXall0MULTIPLE SOURCES
2Beta-arrestin-1COMPLEX#11RECOMBINANT
3C-X-C chemokine receptor type 4COMPLEX#21SYNTHETIC
4Fab30COMPLEX#3-#41RECOMBINANT
Molecular weightValue: 0.19 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Rattus norvegicus (Norway rat)10116
24Mus musculus (house mouse)10090
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
34Escherichia 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 46000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5637
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: 3236193
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53387 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8GO8

8go8


Accession code: 8GO8 / Source name: PDB / Type: experimental model

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