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- EMDB-35106: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: EMDB / ID: EMD-35106
TitleStructure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 (Local refine)
Map data
Sample
  • Complex: Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refine
    • Complex: Beta arrestin 1
      • Protein or peptide: Beta-arrestin-1
    • Complex: CXC chemokine receptor type 4 phosphopeptide
      • Protein or peptide: C-X-C chemokine receptor type 4
    • Complex: Fab30
      • Protein or peptide: Fab30 Heavy Chain
      • Protein or peptide: Fab30 Light Chain
KeywordsGPCR / 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 / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid 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 / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid binding / positive regulation of macrophage migration inhibitory factor signaling pathway / Lysosome Vesicle Biogenesis / Ub-specific processing proteases / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway / Specification of primordial germ cells / regulation of inositol trisphosphate biosynthetic process / AP-2 adaptor complex binding / angiotensin receptor binding / MAP2K and MAPK activation / Golgi Associated Vesicle Biogenesis / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / C-X-C chemokine receptor activity / positive regulation of vasculature development / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-cargo adaptor activity / Signaling by ROBO receptors / negative regulation of interleukin-8 production / Formation of definitive endoderm / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / regulation of G protein-coupled receptor signaling pathway / C-C chemokine binding / arrestin family protein binding / G protein-coupled receptor internalization / anchoring junction / mitogen-activated protein kinase kinase binding / sensory perception / Thrombin signalling through proteinase activated receptors (PARs) / Chemokine receptors bind chemokines / dendritic cell chemotaxis / clathrin binding / stress fiber assembly / response to morphine / positive regulation of Rho protein signal transduction / cellular response to cytokine stimulus / cell leading edge / negative regulation of interleukin-6 production / pseudopodium / positive regulation of oligodendrocyte differentiation / positive regulation of receptor internalization / phototransduction / negative regulation of Notch signaling pathway / Binding and entry of HIV virion / cysteine-type endopeptidase inhibitor activity / regulation of cell adhesion / coreceptor activity / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / neurogenesis / positive regulation of protein ubiquitination / nuclear estrogen receptor binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / GTPase activator activity / cell chemotaxis / ubiquitin binding / calcium-mediated signaling / phosphoprotein binding / brain development / negative regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to virus / endocytosis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / late endosome / protein transport / positive regulation of cold-induced thermogenesis / virus receptor activity / positive regulation of cytosolic calcium ion concentration / actin binding / cytoplasmic vesicle / regulation of apoptotic process / G alpha (i) signalling events / molecular adaptor activity / 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 / response to hypoxia / early endosome / positive regulation of ERK1 and ERK2 cascade / postsynaptic membrane
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 / Chemokine receptor family / Arrestin-like, N-terminal / Arrestin C-terminal-like 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 / Chemokine receptor family / 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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 Å
AuthorsMaharana J / Sarma P / Yadav MK / Banerjee R / Shukla AK
Funding support India, 1 items
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 MK / Banerjee R / Shukla AK
History
DepositionJan 11, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35106.png

Downloads & links

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Map

FileDownload / File: emd_35106.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 256 pix.
= 421.453 Å		1.65 Å/pix.
x 256 pix.
= 421.453 Å		1.65 Å/pix.
x 256 pix.
= 421.453 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6463 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.38712916 - 1.4142554
Average (Standard dev.)-0.00006419709 (±0.018982843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 421.4528 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35106_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_35106_half_map_2.map
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Sample components

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Entire : Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refine

EntireName: Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refine
Components
  • Complex: Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refine
    • Complex: Beta arrestin 1
      • Protein or peptide: Beta-arrestin-1
    • Complex: CXC chemokine receptor type 4 phosphopeptide
      • Protein or peptide: C-X-C chemokine receptor type 4
    • Complex: Fab30
      • Protein or peptide: Fab30 Heavy Chain
      • Protein or peptide: Fab30 Light Chain

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Supramolecule #1: Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refine

SupramoleculeName: Peptide5 bound beta-arrestin1 in complex with Fab30 - Local refine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 190 KDa

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Supramolecule #2: Beta arrestin 1

SupramoleculeName: Beta arrestin 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: CXC chemokine receptor type 4 phosphopeptide

SupramoleculeName: CXC chemokine receptor type 4 phosphopeptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 / Details: Chemically synthesized
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Supramolecule #4: Fab30

SupramoleculeName: Fab30 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 47.088508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI RKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ESETPVDTNL IELDTNDDDI VFEDFARQRL KGMK DDKDE EDDGTGSPHL NNR

UniProtKB: Beta-arrestin-1

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Macromolecule #2: Fab30 Heavy Chain

MacromoleculeName: Fab30 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.512354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH

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Macromolecule #3: Fab30 Light Chain

MacromoleculeName: Fab30 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: C-X-C chemokine receptor type 4

MacromoleculeName: C-X-C chemokine receptor type 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.38053 KDa
SequenceString:
GHSSV(SEP)(TPO)E(SEP)E (SEP)(SEP)(SEP)FH(SEP)(SEP)

UniProtKB: C-X-C chemokine receptor type 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
300.0 mMNaClSodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP / Details: Blotted for 3 seconds before plunging..

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 5637 / Average electron dose: 49.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 46000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3236193
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8gp3

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 86525
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8gp3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8i0q:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 (Local refine)

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