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- EMDB-64049: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64049
TitleCryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
Map data
Sample
  • Complex: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: scFv30
    • Protein or peptide: Adhesion G protein-coupled receptor E1
    • Protein or peptide: Adhesion G protein-coupled receptor E1
Keywordscomplex / membrane protein / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZhong YN
Funding support China, 1 items
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 YN
History
DepositionApr 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64049.png

Downloads & links

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Map

FileDownload / File: emd_64049.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.02
Minimum - Maximum-0.1242938 - 17.233191999999999
Average (Standard dev.)-0.005560029 (±0.5252262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64049_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64049_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64049_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex

EntireName: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
Components
  • Complex: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: scFv30
    • Protein or peptide: Adhesion G protein-coupled receptor E1
    • Protein or peptide: Adhesion G protein-coupled receptor E1

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Supramolecule #1: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex

SupramoleculeName: Cryo-EM structure of ADGRE1-beta arrestin1-scFv30 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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
Details: Sequence reference for Mus musculus is not available at the time of biocuration. Current sequence reference is from UniProt id P17870.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 42.177195 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD IVLFNTA QYKVPVAMEE ADDTVAPSST FSKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSSVAVE LPFTLMHPKP KEEPPHREVP EHETPVDTNL

UniProtKB: Beta-arrestin-1

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Macromolecule #2: scFv30

MacromoleculeName: scFv30 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 26.986742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG LEWVASISSY YGYTYYADSV KGRFTISADT SKNTAYLQMN SLRAEDTAVY YCARSRQFWY SGLDYWGQGT LV TVSSAHH HHHH

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Macromolecule #3: Adhesion G protein-coupled receptor E1

MacromoleculeName: Adhesion G protein-coupled receptor E1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.563835 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ANLAIIMASG ELTME

UniProtKB: Adhesion G protein-coupled receptor E1

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Macromolecule #4: Adhesion G protein-coupled receptor E1

MacromoleculeName: Adhesion G protein-coupled receptor E1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 32.333805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FSLYIISHVG TVISLVCLAL AIATFLLCRA VQNHNTYMHL HLCVCLFLAK ILFLTGIDKT DNQTACAIIA GFLHYLFLAC FFWMLVEAV MLFLMVRNLK VVNYFSSRNI KMLHLCAFGY GLPVLVVIIS ASVQPRGYGM HNRCWLNTET GFIWSFLGPV C MIITINSV ...String:
FSLYIISHVG TVISLVCLAL AIATFLLCRA VQNHNTYMHL HLCVCLFLAK ILFLTGIDKT DNQTACAIIA GFLHYLFLAC FFWMLVEAV MLFLMVRNLK VVNYFSSRNI KMLHLCAFGY GLPVLVVIIS ASVQPRGYGM HNRCWLNTET GFIWSFLGPV C MIITINSV LLAWTLWVLR QKLCSVSSEV SKLKDTRLLT FKAIAQIFIL GCSWVLGIFQ IGPLASIMAW LFTIINSLQG AF IFLIHCL LNRQVRDEYK KLLTRKTDLS SHSQTSGILL SSMPSTSKMG

UniProtKB: Adhesion G protein-coupled receptor E1

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.875 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140558
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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