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- PDB-9v38: Structure of C5a anaphylatoxin chemotactic receptor 2, C5aR2 boun... -

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Basic information

Entry
Database: PDB / ID: 9v38
TitleStructure of C5a anaphylatoxin chemotactic receptor 2, C5aR2 bound to EP54
Components
  • C5a anaphylatoxin chemotactic receptor 2
  • EP54 ligand
KeywordsSIGNALING PROTEIN / G protein coupled receptor / G protein / Membrane protein / Immunite system
Function / homology
Function and homology information


regulation of interleukin-8 production / complement component C5a receptor activity / negative regulation of neutrophil chemotaxis / complement receptor mediated signaling pathway / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / Regulation of Complement cascade / basal plasma membrane / Peptide ligand-binding receptors / G protein-coupled receptor activity ...regulation of interleukin-8 production / complement component C5a receptor activity / negative regulation of neutrophil chemotaxis / complement receptor mediated signaling pathway / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / Regulation of Complement cascade / basal plasma membrane / Peptide ligand-binding receptors / G protein-coupled receptor activity / chemotaxis / apical part of cell / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / inflammatory response / plasma membrane
Similarity search - Function
Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
C5a anaphylatoxin chemotactic receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsTiwari, D. / Sano, F.K. / Yadav, M.K. / Sawada, K. / Ganguly, M. / Mishra, S. / Dalal, A. / Banerjee, R. / Nureki, O. / Shukla, A.K.
Funding support United Kingdom, India, 3items
OrganizationGrant numberCountry
Wellcome TrustIA/S/20/1/504916 United Kingdom
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Science and Engineering Research Board (SERB)CRG/2022/002646 India
CitationJournal: Mol.Cell / Year: 2026
Title: Molecular mechanisms of naturally encoded signaling bias at the complement anaphylatoxin receptors.
Authors: Tiwari, D. / Sawada, K. / Dalal, A. / Mishra, S. / Li, X.X. / Dent, J.C. / Kim, K. / Yadav, M.K. / Roy, N. / Ganguly, M. / Banerjee, N. / Stepniewski, T.M. / Ahn, D. / Yamaguchi, K. / ...Authors: Tiwari, D. / Sawada, K. / Dalal, A. / Mishra, S. / Li, X.X. / Dent, J.C. / Kim, K. / Yadav, M.K. / Roy, N. / Ganguly, M. / Banerjee, N. / Stepniewski, T.M. / Ahn, D. / Yamaguchi, K. / Oshima, H.S. / Hashimoto, K. / Fung, J.N. / Lerskiatiphanich, T. / Cui, C.S. / Lee, J.D. / Selent, J. / Inoue, A. / Clark, R.J. / Chung, K.Y. / Banerjee, R. / Sano, F.K. / Woodruff, T.M. / Nureki, O. / Shukla, A.K.
History
DepositionMay 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: C5a anaphylatoxin chemotactic receptor 2
C: EP54 ligand


Theoretical massNumber of molelcules
Total (without water)43,2262
Polymers43,2262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein C5a anaphylatoxin chemotactic receptor 2 / Complement component 5a receptor 2 / G-protein coupled receptor 77


Mass: 42014.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5AR2, C5L2, GPR77 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9P296
#2: Protein/peptide EP54 ligand


Mass: 1211.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C5aR2 bound to EP54 ligand / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 63.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPUimage acquisition
4cryoSPARC4.6.2CTF correction
7Coot0.9.6model fitting
9PHENIXmodel refinement
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214174 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: SwissModel / Type: in silico model

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