8HPT

Structure of C5a-pep bound mouse C5aR1 in complex with Go


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of anaphylatoxin binding, activation, and signaling bias at complement receptors.

Yadav, M.K.Maharana, J.Yadav, R.Saha, S.Sarma, P.Soni, C.Singh, V.Saha, S.Ganguly, M.Li, X.X.Mohapatra, S.Mishra, S.Khant, H.A.Chami, M.Woodruff, T.M.Banerjee, R.Shukla, A.K.Gati, C.

(2023) Cell 186: 4956-4973.e21

  • DOI: https://doi.org/10.1016/j.cell.2023.09.020
  • Primary Citation of Related Structures:  
    8HPT, 8HQC, 8I95, 8I97, 8I9A, 8I9L, 8I9S, 8IA2, 8J6D, 8JZZ

  • PubMed Abstract: 

    The complement system is a critical part of our innate immune response, and the terminal products of this cascade, anaphylatoxins C3a and C5a, exert their physiological and pathophysiological responses primarily via two GPCRs, C3aR and C5aR1. However, the molecular mechanism of ligand recognition, activation, and signaling bias of these receptors remains mostly elusive. Here, we present nine cryo-EM structures of C3aR and C5aR1 activated by their natural and synthetic agonists, which reveal distinct binding pocket topologies of complement anaphylatoxins and provide key insights into receptor activation and transducer coupling. We also uncover the structural basis of a naturally occurring mechanism to dampen the inflammatory response of C5a via proteolytic cleavage of the terminal arginine and the G-protein signaling bias elicited by a peptide agonist of C3aR identified here. In summary, our study elucidates the innerworkings of the complement anaphylatoxin receptors and should facilitate structure-guided drug discovery to target these receptors in a spectrum of disorders.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C5a anaphylatoxin chemotactic receptor 1407Mus musculusMutation(s): 0 
Gene Names: C5ar1C5arC5r1
Membrane Entity: Yes 
UniProt
Find proteins for P30993 (Mus musculus)
Explore P30993 
Go to UniProtKB:  P30993
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UniProt GroupP30993
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MEA-LYS-PRO-ZAL-ALC-DARB [auth D]6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alphaC [auth B]240Homo sapiensMutation(s): 6 
Gene Names: GNAO1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens)
Explore P09471 
Go to UniProtKB:  P09471
GTEx:  ENSG00000087258 
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UniProt GroupP09471
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth C]338Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]56Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody fragment ScFv16F [auth H]256Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALC
Query on ALC
B [auth D]L-PEPTIDE LINKINGC9 H17 N O2ALA
MEA
Query on MEA
B [auth D]L-PEPTIDE LINKINGC10 H13 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR29041/BRB/10/1697/20

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-07-17
    Changes: Data collection, Database references