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- EMDB-60785: Structure of JR14a-bound human C3aR -

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Basic information

Entry
Database: EMDB / ID: EMD-60785
TitleStructure of JR14a-bound human C3aR
Map datafocused refined sharp map of C3aR1-JR14a
Sample
  • Complex: C3aR-JR14A
    • Protein or peptide: C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
  • Ligand: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


complement component C3a receptor activity / complement component C5a receptor activity / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / blood circulation / azurophil granule membrane / positive regulation of macrophage chemotaxis / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / specific granule membrane ...complement component C3a receptor activity / complement component C5a receptor activity / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / blood circulation / azurophil granule membrane / positive regulation of macrophage chemotaxis / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / specific granule membrane / Peptide ligand-binding receptors / Regulation of Complement cascade / calcium-mediated signaling / electron transport chain / G protein-coupled receptor activity / positive regulation of angiogenesis / chemotaxis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / heme binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
C3a anaphylatoxin chemotactic receptor / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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)
Similarity search - Domain/homology
Soluble cytochrome b562 / C3a anaphylatoxin chemotactic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 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 12, 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_60785.png

Downloads & links

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Map

FileDownload / File: emd_60785.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused refined sharp map of C3aR1-JR14a
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.063
Minimum - Maximum-0.6109903 - 0.92482543
Average (Standard dev.)-0.00006034677 (±0.0073195775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Non-uniform refined sharp map of C3aR1-JR14a-bRIL-Fab-Nb

Fileemd_60785_additional_1.map
AnnotationNon-uniform refined sharp map of C3aR1-JR14a-bRIL-Fab-Nb
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half-map-A

Fileemd_60785_half_map_1.map
Annotationhalf-map-A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half-map-B

Fileemd_60785_half_map_2.map
Annotationhalf-map-B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : C3aR-JR14A

EntireName: C3aR-JR14A
Components
  • Complex: C3aR-JR14A
    • Protein or peptide: C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
  • Ligand: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid

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Supramolecule #1: C3aR-JR14A

SupramoleculeName: C3aR-JR14A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.4 kDa/nm

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Macromolecule #1: C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562

MacromoleculeName: C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.608289 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAID ASFSAETNST DLLSQPWNEP PVILSMVILS LTFLLGLPGN GLVLWVAGLK MQRTVNTIWF LHLTLADLLC CLSLPFSLA HLALQGQWPY GRFLCKLIPS IIVLNMFASV FLLTAISLDR CLVVFKPIWC QNHRNVGMAC SICGCIWVVA F VMCIPVFV ...String:
DYKDDDDAID ASFSAETNST DLLSQPWNEP PVILSMVILS LTFLLGLPGN GLVLWVAGLK MQRTVNTIWF LHLTLADLLC CLSLPFSLA HLALQGQWPY GRFLCKLIPS IIVLNMFASV FLLTAISLDR CLVVFKPIWC QNHRNVGMAC SICGCIWVVA F VMCIPVFV YREIFTTDNH NRCGYKFGLS SSLDYPDFYG DPLENRSLEN IVQPPGEMND RLDPSSFQTN DHPWTVPTVF QP QTFQRPS ADSLPRGSAR LTSQNLYSNV FKPADVVSPK IPSGFPIEDH ETSPLDNSDA FLSTHLKLFP SASSNSFYES ELP QGFQDY YNLGQFTDDD QVPTPLVAIT ITRLVVGFLL PSVIMIACYS FIVFRMQRAR RQLADLEDNW ETLNDNLKVI EKAD NAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGFD ILVGQIDDAL KLANEGKVKE AQAAAEQLKT TRNAY IQKY LERARSTLKS QSKTFRVAVV VVAVFLVCWT PYHIFGVLSL LTDPETPLGK TLMSWDHVCI ALASANSCFN PFLYAL LGK DFRKKARQSI QGILEAAFSE ELTRSTHCPS NNVISERNST TVASLEVLFQ

UniProtKB: C3a anaphylatoxin chemotactic receptor, Soluble cytochrome b562, C3a anaphylatoxin chemotactic receptor

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Macromolecule #2: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl...

MacromoleculeName: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1D9A
Molecular weightTheoretical: 533.47 Da

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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: GATAN K3 BIOQUANTUM (6k 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: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 342058
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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