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- PDB-9v3c: Structure of C5a anaphylatoxin chemotactic receptor 2, C5aR2 boun... -

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Basic information

Entry
Database: PDB / ID: 9v3c
TitleStructure of C5a anaphylatoxin chemotactic receptor 2, C5aR2 bound to C5a
Components
  • C5a anaphylatoxin
  • C5a anaphylatoxin chemotactic receptor 2
KeywordsSIGNALING PROTEIN / G protein coupled receptor / G protein / Membrane protein / Immunite system
Function / homology
Function and homology information


regulation of interleukin-8 production / Terminal pathway of complement / membrane attack complex / complement component C5a receptor activity / negative regulation of neutrophil chemotaxis / Activation of C3 and C5 / complement activation, GZMK pathway / negative regulation of macrophage chemotaxis / other organism cell membrane / complement receptor mediated signaling pathway ...regulation of interleukin-8 production / Terminal pathway of complement / membrane attack complex / complement component C5a receptor activity / negative regulation of neutrophil chemotaxis / Activation of C3 and C5 / complement activation, GZMK pathway / negative regulation of macrophage chemotaxis / other organism cell membrane / complement receptor mediated signaling pathway / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / complement activation, classical pathway / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine 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 / killing of cells of another organism / G alpha (i) signalling events / basolateral plasma membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement component 5, CUB domain / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin ...: / Complement component 5, CUB domain / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C5 / C5a anaphylatoxin chemotactic receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 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
A: C5a anaphylatoxin chemotactic receptor 2
D: C5a anaphylatoxin


Theoretical massNumber of molelcules
Total (without water)50,3032
Polymers50,3032
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 C5a anaphylatoxin


Mass: 8288.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01031
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 C5a / 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: 64.3 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: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36285 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: SwissModel / Type: in silico model

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