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- EMDB-35104: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: EMDB / ID: EMD-35104
TitleStructure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine)
Map dataFull map
Sample
  • Complex: Peptide 1 bound beta-arrestin1 in complex with Fab30 - Local refine
    • Complex: beta-arrestin1
      • Protein or peptide: Beta-arrestin-1Arrestin
    • Complex: C5a anaphylatoxin chemotactic receptor 1
      • Protein or peptide: C5a anaphylatoxin chemotactic receptor 1
    • Complex: Fab30
      • Protein or peptide: Fab30 heavy chain
      • Protein or peptide: Fab30 light chain
Function / homology
Function and homology information


V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / complement component C5a receptor activity ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / complement component C5a receptor activity / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / response to peptidoglycan / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / positive regulation of smooth muscle cell apoptotic process / sensory perception of chemical stimulus / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / complement receptor mediated signaling pathway / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / response to morphine / positive regulation of neutrophil chemotaxis / Thrombin signalling through proteinase activated receptors (PARs) / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / positive regulation of macrophage chemotaxis / stress fiber assembly / negative regulation of Notch signaling pathway / amyloid-beta clearance / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of receptor internalization / phototransduction / : / positive regulation of vascular endothelial growth factor production / cellular defense response / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / Peptide ligand-binding receptors / GTPase activator activity / neutrophil chemotaxis / secretory granule membrane / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / Regulation of Complement cascade / positive regulation of epithelial cell proliferation / G protein-coupled receptor activity / G protein-coupled receptor binding / astrocyte activation / nuclear estrogen receptor binding / phosphoprotein binding / microglial cell activation / mRNA transcription by RNA polymerase II / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / cognition / endocytosis / positive regulation of angiogenesis / chemotaxis / protein transport / apical part of cell / positive regulation of peptidyl-serine phosphorylation / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / postsynaptic membrane / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / dendritic spine / positive regulation of MAPK cascade / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / endosome / defense response to Gram-positive bacterium / response to xenobiotic stimulus / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding
Similarity search - Function
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 ...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. / 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
C5a anaphylatoxin chemotactic receptor 1 / Beta-arrestin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 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
CitationJournal: 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-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35104.png

Downloads & links

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Map

FileDownload / File: emd_35104.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Voxel sizeX=Y=Z: 1.3667 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4821484 - 2.892706
Average (Standard dev.)0.00034851575 (±0.039538465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 393.60962 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_35104_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_35104_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Peptide 1 bound beta-arrestin1 in complex with Fab30 - Local refine

EntireName: Peptide 1 bound beta-arrestin1 in complex with Fab30 - Local refine
Components
  • Complex: Peptide 1 bound beta-arrestin1 in complex with Fab30 - Local refine
    • Complex: beta-arrestin1
      • Protein or peptide: Beta-arrestin-1Arrestin
    • Complex: C5a anaphylatoxin chemotactic receptor 1
      • Protein or peptide: C5a anaphylatoxin chemotactic receptor 1
    • Complex: Fab30
      • Protein or peptide: Fab30 heavy chain
      • Protein or peptide: Fab30 light chain

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

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

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Supramolecule #2: beta-arrestin1

SupramoleculeName: beta-arrestin1 / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: C5a anaphylatoxin chemotactic receptor 1

SupramoleculeName: C5a anaphylatoxin chemotactic receptor 1 / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #4 / Details: Chemically synthesized
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Fab30

SupramoleculeName: Fab30 / type: complex / ID: 4 / Chimera: Yes / 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

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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: C5a anaphylatoxin chemotactic receptor 1

MacromoleculeName: C5a anaphylatoxin chemotactic receptor 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.69834 KDa
SequenceString:
E(SEP)K(SEP)F(TPO)R(SEP)(TPO)V D(TPO)MAQKTQAV

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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 chlorideSodium 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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6212 / Average electron dose: 56.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4304237
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4jqi

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 80437
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8go8

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8i0n:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine)

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