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- EMDB-60784: Focused refinement map of C3aR in JR14A-C3aR-Gi-scFv16 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60784
TitleFocused refinement map of C3aR in JR14A-C3aR-Gi-scFv16 complex
Map dataReceptor-focused map of C3AR1-Gi-scFv16 complex with JR14A
Sample
  • Complex: C3AR1-Gi complex
    • Protein or peptide: C3aR
KeywordsGPCR / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKim J / Ko S / Choi H-J
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2023R1A2C300420512 Korea, Republic Of
CitationJournal: EMBO J / Year: 2025
Title: Structural insights into small-molecule agonist recognition and activation of complement receptor C3aR.
Authors: Jinuk Kim / Saebom Ko / Chulwon Choi / Jungnam Bae / Hyeonsung Byeon / Chaok Seok / Hee-Jung Choi /
Abstract: The complement system plays crucial roles in innate immunity and inflammatory responses. The anaphylatoxin C3a mediates pro-inflammatory and chemotactic functions through the G protein-coupled ...The complement system plays crucial roles in innate immunity and inflammatory responses. The anaphylatoxin C3a mediates pro-inflammatory and chemotactic functions through the G protein-coupled receptor C3aR. While the active structure of the C3a-C3aR-G complex has been determined, the inactive conformation and activation mechanism of C3aR remain elusive. Here we report the cryo-EM structure of ligand-free, G protein-free C3aR, providing insights into its inactive conformation. In addition, we determine the structures of C3aR in complex with the synthetic small-molecule agonist JR14a in two distinct conformational states: a G protein-free intermediate, and a fully active G-bound state. The structure of the active JR14a-bound C3aR reveals that JR14a engages in highly conserved interactions with C3aR, similar to the binding of the C-terminal pentapeptide of C3a, along with JR14a-specific interactions. Structural comparison of C3aR in the apo, intermediate, and fully active states provides novel insights into the conformational landscape and activation mechanism of C3aR and defines a molecular basis explaining its high basal activity. Our results may aid in the rational design of therapeutics targeting complement-related inflammatory disorders.
History
DepositionJul 11, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60784.png

Downloads & links

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Map

FileDownload / File: emd_60784.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReceptor-focused map of C3AR1-Gi-scFv16 complex with JR14A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 324. Å		0.81 Å/pix.
x 400 pix.
= 324. Å		0.81 Å/pix.
x 400 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.7300549 - 1.0194886
Average (Standard dev.)0.0000027265964 (±0.008779246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A map of Receptor-focused map

Fileemd_60784_half_map_1.map
AnnotationHalf A map of Receptor-focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of Receptor-focused map

Fileemd_60784_half_map_2.map
AnnotationHalf B map of Receptor-focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C3AR1-Gi complex

EntireName: C3AR1-Gi complex
Components
  • Complex: C3AR1-Gi complex
    • Protein or peptide: C3aR

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Supramolecule #1: C3AR1-Gi complex

SupramoleculeName: C3AR1-Gi complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 kDa/nm

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Macromolecule #1: C3aR

MacromoleculeName: C3aR / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDASI D MASFSAET NSTDLLSQPW NEPPVILSMV ILSLTFLLGL PGNGLVLWVA GLKMQRTVNT IWFLHLTLAD LLCCLSLPFS LAHLALQGQW PYGRFLCKLI PSIIVLNMFA SVFLLTAISL DRCLVVFKPI WCQNHRNVGM ACSICGCIWV VAFVMCIPVF ...String:
DYKDDDDASI D MASFSAET NSTDLLSQPW NEPPVILSMV ILSLTFLLGL PGNGLVLWVA GLKMQRTVNT IWFLHLTLAD LLCCLSLPFS LAHLALQGQW PYGRFLCKLI PSIIVLNMFA SVFLLTAISL DRCLVVFKPI WCQNHRNVGM ACSICGCIWV VAFVMCIPVF VYREIFTTDN HNRCGYKFGL SSSLDYPDFY GDPLENRSLE NIVQPPGEMN DRLDPSSFQT NDHPWTVPTV FQPQTFQRPS ADSLPRGSAR LTSQNLYSNV FKPADVVSPK IPSGFPIEDH ETSPLDNSDA FLSTHLKLFP SASSNSFYES ELPQGFQDYY NLGQFTDDDQ VPTPLVAITI TRLVVGFLLP SVIMIACYSF IVFRMQRGRF AKSQSKTFRV AVVVVAVFLV CWTPYHIFGV LSLLTDPETP LGKTLMSWDH VCIALASANS CFNPFLYALL GKDFRKKARQ SIQGILEAAF SEELTRSTHC PSNNVISERN STTV ASLEV LFQ

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338234
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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