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- PDB-9uco: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex -

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Basic information

Entry
Database: PDB / ID: 9uco
TitleCryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
Components
  • (Adhesion G protein-coupled receptor E1) x 2
  • Beta-arrestin-1
  • scFv30
KeywordsMEMBRANE PROTEIN / complex / ADGRE1
Function / homology
Function and homology information


Class B/2 (Secretin family receptors) / TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis ...Class B/2 (Secretin family receptors) / TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin heavy chain binding / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / desensitization of G protein-coupled receptor signaling pathway / acetylcholine receptor binding / G protein-coupled receptor internalization / inositol hexakisphosphate binding / sensory perception / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / small molecule binding / phosphatidylinositol-3,4,5-trisphosphate binding / pseudopodium / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / cell periphery / positive regulation of protein phosphorylation / receptor internalization / G protein-coupled receptor binding / G protein-coupled receptor activity / protein transport / cytoplasmic vesicle / molecular adaptor activity / ubiquitin-dependent protein catabolic process / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / external side of plasma membrane / calcium ion binding / signal transduction / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GPCR family 2, EMR1-like receptor / GPCR proteolysis site, GPS, motif / GAIN domain superfamily / : / GPS motif / G-protein-coupled receptor proteolytic site domain / GAIN-B domain profile. / Arrestin, conserved site / Arrestins signature. / Arrestin ...GPCR family 2, EMR1-like receptor / GPCR proteolysis site, GPS, motif / GAIN domain superfamily / : / GPS motif / G-protein-coupled receptor proteolytic site domain / GAIN-B domain profile. / 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 / : / Calcium-binding EGF domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin E-set
Similarity search - Domain/homology
Beta-arrestin-1 / Adhesion G protein-coupled receptor E1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZhong, Y.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
Authors: Zhong, Y.N.
History
DepositionApr 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
B: scFv30
F: scFv30
C: Beta-arrestin-1
D: scFv30
E: scFv30
L: Adhesion G protein-coupled receptor E1
R: Adhesion G protein-coupled receptor E1
G: Adhesion G protein-coupled receptor E1
H: Adhesion G protein-coupled receptor E1


Theoretical massNumber of molelcules
Total (without water)260,09710
Polymers260,09710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Beta-arrestin-1 / Arrestin beta-1 / Arrestin-2


Mass: 42177.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Mus musculus is not available at the time of biocuration. Current sequence reference is from UniProt id P17870.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17870
#2: Antibody
scFv30


Mass: 26986.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein/peptide Adhesion G protein-coupled receptor E1 / Cell surface glycoprotein F4/80 / EGF-like module receptor 1 / EGF-like module-containing mucin- ...Cell surface glycoprotein F4/80 / EGF-like module receptor 1 / EGF-like module-containing mucin-like hormone receptor-like 1 / EMR1 hormone receptor


Mass: 1563.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgre1, Emr1, Gpf480 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q61549
#4: Protein Adhesion G protein-coupled receptor E1 / Cell surface glycoprotein F4/80 / EGF-like module receptor 1 / EGF-like module-containing mucin- ...Cell surface glycoprotein F4/80 / EGF-like module receptor 1 / EGF-like module-containing mucin-like hormone receptor-like 1 / EMR1 hormone receptor


Mass: 32333.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgre1, Emr1, Gpf480 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q61549
Has protein modificationY

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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

ComponentName: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
31Bos taurus (domestic cattle)9913
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.875 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140558 / Symmetry type: POINT
RefinementHighest resolution: 3.58 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512499
ELECTRON MICROSCOPYf_angle_d0.66917104
ELECTRON MICROSCOPYf_dihedral_angle_d4.521755
ELECTRON MICROSCOPYf_chiral_restr0.0432063
ELECTRON MICROSCOPYf_plane_restr0.0062132

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