9KXS | pdb_00009kxs

Structure of EP67 bound mouse C5aR1 in complex with Go


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural basis of complement anaphylatoxin receptor activation by an immunostimulant lead candidate.

Dalal, A.Yadav, M.K.Ganguly, M.Mishra, S.Yadav, R.Sinha, S.Roy, N.Tiwari, D.Mukherjee, D.Reyaz, A.Dsouza, C.A.Nigam, A.Banerjee, N.Li, X.X.Clark, R.J.Woodruff, T.M.Banerjee, R.Gati, C.Shukla, A.K.

(2026) Proc Natl Acad Sci U S A 123: e2614459123-e2614459123

  • DOI: https://doi.org/10.1073/pnas.2614459123
  • Primary Citation Related Structures: 
    9KUG, 9KXS, 9KZ2, 9KZ8

  • PubMed Abstract: 

    Activation of the complement cascade is a primary innate immune response mechanism to combat pathogenic infections. Complement anaphylatoxins (i.e., C3a and C5a) exert a robust inflammatory response via prototypical GPCRs (i.e., C3aR and C5aR1). Several peptides derived from anaphylatoxins have shown promise as immunostimulants from therapeutic standpoint by eliciting immune response without excessive inflammation. EP67, a C5a-derived decapeptide, is the most advanced candidate with preclinical indications in antiviral and antibacterial context. Still, the molecular mechanism and the precise receptor target of EP67 remain unclear. Here, we perform a comprehensive pharmacological profiling of EP67 on the human and mouse C3aR and C5aR1 and find that it preferentially activates human C3aR in transducer-coupling assays. Subsequently, we determined four cryo-EM structures of C3aR and C5aR1 in complex with EP67, which elucidate the molecular details of its interaction with, and activation of, these receptors. Interestingly, we observe that EP67 adopts a hook-like structure and binds in the orthosteric pocket of the receptors, analogous to that of the carboxyl terminus of C3a and C5a. We employ site-directed mutagenesis studies to validate the key interactions of EP67 with these receptors and corroborate the structural observations including the engagement of a critical activation switch. Finally, we observe that EP67 induces distinct conformations of the TM7-Helix8 interface for C3aR and C5aR1, which provides a plausible explanation for its ability to preferentially activate C3aR. In summary, our study elucidates molecular insights into the interaction of EP67 with the complement anaphylatoxin receptors, and it should facilitate further optimization for therapeutic applications.


  • Organizational Affiliation
    • Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.

Macromolecule Content 

  • Total Structure Weight: 146.96 kDa 
  • Atom Count: 8,152 
  • Modeled Residue Count: 1,119 
  • Deposited Residue Count: 1,334 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1407Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: CHRM4C5ar1C5arC5r1
UniProt & NIH Common Fund Data Resources
Find proteins for P08173 (Homo sapiens)
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Go to UniProtKB:  P08173
PHAROS:  P08173
GTEx:  ENSG00000180720 
Find proteins for P30993 (Mus musculus)
Explore P30993 
Go to UniProtKB:  P30993
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP30993P08173
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alpha240Homo sapiensMutation(s): 6 
Gene Names: GNAO1
EC: 3.6.5
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Find proteins for P09471 (Homo sapiens)
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Go to UniProtKB:  P09471
PHAROS:  P09471
GTEx:  ENSG00000087258 
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UniProt GroupP09471
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1350Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody fragment ScFv16E [auth H]256Mus musculusMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
EP67 ligandF [auth D]10Homo sapiensMutation(s): 0 
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DAL
Query on DAL
F [auth D]D-PEPTIDE LINKINGC3 H7 N O2

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MLE
Query on MLE
F [auth D]L-PEPTIDE LINKINGC7 H15 N O2LEU

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.5.3

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaIPA/2020/000405
Wellcome TrustUnited KingdomIA/S/20/1/504916
Science and Engineering Research Board (SERB)IndiaCRG/2022/002646

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Data collection, Database references