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- EMDB-34188: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: EMDB / ID: EMD-34188
TitleStructure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4
Map dataFull map with pixel size 0.878.
Sample
  • Complex: Peptide5 bound beta-arrestin1 in complex with Fab30
    • Complex: Beta-arrestin-1
      • Protein or peptide: Beta-arrestin-1
    • Complex: C-X-C chemokine receptor type 4
      • 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
Function / homology
Function and homology information


V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / G alpha (s) signalling events / regulation of viral process / alpha-1B adrenergic receptor binding / positive regulation of vascular wound healing / follicle-stimulating hormone signaling pathway ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / G alpha (s) signalling events / regulation of viral process / 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 / 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 / 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 / endothelial cell differentiation / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / Signaling by ROBO receptors / regulation of chemotaxis / : / positive regulation of dendrite extension / Formation of definitive endoderm / positive regulation of chemotaxis / 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 / response to morphine / Chemokine receptors bind chemokines / Thrombin signalling through proteinase activated receptors (PARs) / anchoring junction / dendritic cell chemotaxis / mitogen-activated protein kinase kinase binding / clathrin binding / positive regulation of oligodendrocyte differentiation / positive regulation of Rho protein signal transduction / stress fiber assembly / negative regulation of Notch signaling pathway / cell leading edge / epithelial cell development / pseudopodium / cellular response to cytokine stimulus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / negative regulation of interleukin-6 production / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of receptor internalization / phototransduction / small molecule binding / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / cardiac muscle contraction / clathrin-coated pit / negative regulation of protein ubiquitination / visual perception / GTPase activator activity / neurogenesis / cell chemotaxis / negative regulation of protein phosphorylation / ubiquitin binding / response to activity / positive regulation of protein ubiquitination / G protein-coupled receptor binding / G protein-coupled receptor activity / nuclear estrogen receptor binding / calcium-mediated signaling / phosphoprotein binding / insulin-like growth factor receptor binding / neuron migration / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / brain development / negative regulation of ERK1 and ERK2 cascade / endocytosis / protein transport / cellular response to xenobiotic stimulus
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) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 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
DepositionAug 25, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34188.png

Downloads & links

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Map

FileDownload / File: emd_34188.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map with pixel size 0.878.
Voxel sizeX=Y=Z: 0.878 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.17767604 - 0.33455184
Average (Standard dev.)-0.00003095029 (±0.008018189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 421.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A with pixel size 0.878.

Fileemd_34188_half_map_1.map
AnnotationHalf map A with pixel size 0.878.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B with pixel size 0.878.

Fileemd_34188_half_map_2.map
AnnotationHalf map B with pixel size 0.878.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Peptide5 bound beta-arrestin1 in complex with Fab30

EntireName: Peptide5 bound beta-arrestin1 in complex with Fab30
Components
  • Complex: Peptide5 bound beta-arrestin1 in complex with Fab30
    • Complex: Beta-arrestin-1
      • Protein or peptide: Beta-arrestin-1
    • Complex: C-X-C chemokine receptor type 4
      • 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

SupramoleculeName: Peptide5 bound beta-arrestin1 in complex with Fab30 / 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: C-X-C chemokine receptor type 4

SupramoleculeName: C-X-C chemokine receptor type 4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
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: #3-#4
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: C-X-C chemokine receptor type 4

MacromoleculeName: C-X-C chemokine receptor type 4 / type: protein_or_peptide / ID: 2 / 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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Macromolecule #3: Fab30 Heavy Chain

MacromoleculeName: Fab30 Heavy Chain / type: protein_or_peptide / ID: 3 / 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 #4: Fab30 Light Chain

MacromoleculeName: Fab30 Light Chain / type: protein_or_peptide / ID: 4 / 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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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
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:

8go8

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 53387
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

Initial modelPDB ID:

8go8


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

PDB-8gp3:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4

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