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- PDB-8i0q: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: PDB / ID: 8i0q
TitleStructure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 (Local refine)
Components
  • Beta-arrestin-1Arrestin
  • C-X-C chemokine receptor type 4
  • 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 / Activation of SMO / 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 / Activation of SMO / 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 / positive regulation of macrophage migration inhibitory factor signaling pathway / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / positive regulation of mesenchymal stem cell migration / angiotensin receptor binding / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / myosin light chain 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 / C-C chemokine receptor activity / endothelial tube morphogenesis / endothelial cell differentiation / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / C-C chemokine binding / Signaling by ROBO receptors / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of chemotaxis / positive regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / positive regulation of dendrite extension / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / anchoring junction / Thrombin signalling through proteinase activated receptors (PARs) / Chemokine receptors bind chemokines / dendritic cell chemotaxis / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / positive regulation of oligodendrocyte differentiation / stress fiber assembly / negative regulation of Notch signaling pathway / epithelial cell development / cell leading edge / pseudopodium / cellular response to cytokine stimulus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / negative regulation of interleukin-6 production / regulation of calcium ion transport / positive regulation of receptor internalization / phototransduction / Binding and entry of HIV virion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / clathrin-coated pit / negative regulation of protein ubiquitination / cardiac muscle contraction / insulin-like growth factor receptor binding / visual perception / neurogenesis / GTPase activator activity / cell chemotaxis / negative regulation of protein phosphorylation / response to activity / ubiquitin binding / positive regulation of protein ubiquitination / G protein-coupled receptor binding / G protein-coupled receptor activity / nuclear estrogen receptor binding / calcium-mediated signaling / phosphoprotein binding / brain development / neuron migration / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / endocytosis / cellular response to xenobiotic stimulus / 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: 4.45 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
CitationJournal: 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
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)196,8338
Polymers196,8338
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Beta-arrestin-1 / Arrestin / 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: 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)
#3: 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)
#4: 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
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-IDSourceDetails
1Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refineCOMPLEXall0MULTIPLE SOURCES
2Beta arrestin 1COMPLEX#11RECOMBINANT
3CXC chemokine receptor type 4 phosphopeptideCOMPLEX#41SYNTHETICChemically synthesized
4Fab30COMPLEX#2-#31RECOMBINANT
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 chlorideNaClSodium chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy / 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
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: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86525 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8GP3

8gp3

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