9IPY: JR14a-bound human C3aR

Structure of JR14a-bound human C3aR. Determined by electron microscopy at 3.5 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 1
Atoms: 2,949
Mol. weight: 69.14 kDa
Ligands: A1D9A
Released: 23 Apr 2025

Explore 9IPY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IPY contains 15 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-50	30
α-helix	58-73	16
α-helix	75-83	9
α-helix	93-123	31
α-helix	127-131	5
α-helix	136-159	24
β-strand	162-163	2	1
β-strand	172-173	2	1
α-helix	332-341	10
α-helix	342-346	5
α-helix	347-1024	43
α-helix	1028-1047	20
α-helix	1061-1085	25
α-helix	1090-1097	8
α-helix	1099-402	53
α-helix	408-437	30
α-helix	450-457	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562	R	protein	613	Homo sapiens, Escherichia coli	Q16581 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>9IPY_1 C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562 (chains R)
DYKDDDDAIDASFSAETNSTDLLSQPWNEPPVILSMVILSLTFLLGLPGNGLVLWVAGLK
MQRTVNTIWFLHLTLADLLCCLSLPFSLAHLALQGQWPYGRFLCKLIPSIIVLNMFASVF
LLTAISLDRCLVVFKPIWCQNHRNVGMACSICGCIWVVAFVMCIPVFVYREIFTTDNHNR
CGYKFGLSSSLDYPDFYGDPLENRSLENIVQPPGEMNDRLDPSSFQTNDHPWTVPTVFQP
QTFQRPSADSLPRGSARLTSQNLYSNVFKPADVVSPKIPSGFPIEDHETSPLDNSDAFLS
THLKLFPSASSNSFYESELPQGFQDYYNLGQFTDDDQVPTPLVAITITRLVVGFLLPSVI
MIACYSFIVFRMQRARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQ
KATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAY
IQKYLERARSTLKSQSKTFRVAVVVVAVFLVCWTPYHIFGVLSLLTDPETPLGKTLMSWD
HVCIALASANSCFNPFLYALLGKDFRKKARQSIQGILEAAFSEELTRSTHCPSNNVISER
NSTTVASLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1D9A	(2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-met…	C25 H26 Cl2 N4 O3 S	1

Primary citation

Structural insights into small-molecule agonist recognition and activation of complement receptor C3aR. Kim, J., Ko, S., Choi, C. et al. EMBO J (2025) 44:2803-2826. DOI 10.1038/s44318-025-00429-w · PubMed

Other PDB entries of the same protein (UniProt Q16581 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IPV 2.53 Å, Structure of JR14a-C3aR-Gi-scFv16 complex
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
9KVS 2.81 Å, Structure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)
8IA8 2.86 Å, Cryo-EM structure of C3aR-Gi-scFv16 bound with E7 peptide
8ZWG 2.87 Å, cryoEM structure of JR14a bound C3aR-Gi complex
8I95 2.88 Å, Structure of EP54-C3aR-Go complex
8HK2 2.9 Å, C3aR-Gi-C3a protein complex
8ZWF 3.0 Å, cryoEM structure of JR14a bound C3aR-BRIL-BAG2 complex
8J6D 3.1 Å, Structure of EP141-C3aR-Go complex
8I9L 3.18 Å, Structure of C3a-C3aR-Go complex (Composite map)
8I97 3.19 Å, Structure of Apo-C3aR-Go complex (Glacios)
8HK3 3.2 Å, C3aR-Gi-apo protein complex

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