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- PDB-9kvs: Structure of SB290157 bound to human C3aR in complex with Go (Rec... -

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Basic information

Entry
Database: PDB / ID: 9kvs
TitleStructure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)
ComponentsMuscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
KeywordsSIGNALING PROTEIN / G protein coupled receptor / G protein / Membrane protein / Immunite system
Function / homology
Function and homology information


complement component C3a receptor activity / complement component C5a receptor activity / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / azurophil granule membrane / blood circulation / positive regulation of macrophage chemotaxis ...complement component C3a receptor activity / complement component C5a receptor activity / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / azurophil granule membrane / blood circulation / positive regulation of macrophage chemotaxis / regulation of locomotion / positive regulation of vascular endothelial growth factor production / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / specific granule membrane / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / calcium-mediated signaling / G protein-coupled receptor activity / chemotaxis / positive regulation of angiogenesis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / postsynaptic membrane / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / Neutrophil degranulation / synapse / dendrite / signal transduction / plasma membrane
Similarity search - Function
C3a anaphylatoxin chemotactic receptor / Muscarinic acetylcholine receptor M4 / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Muscarinic acetylcholine receptor family / Formyl peptide receptor-related / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 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
: / Muscarinic acetylcholine receptor M4 / C3a anaphylatoxin chemotactic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsBanerjee, R. / Sano, F.K. / Yadav, M.K. / Sawada, K. / Ganguly, M. / Mishra, S. / Dalal, A. / 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: To Be Published
Title: Structure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)
Authors: Banerjee, R. / Sano, F.K. / Yadav, M.K. / Sawada, K. / Ganguly, M. / Mishra, S. / Dalal, A. / Nureki, O. / Shukla, A.K.
History
DepositionDec 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 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
C: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2212
Polymers59,8081
Non-polymers4121
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 Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor / C3AR / C3a-R


Mass: 59808.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM4, C3AR1, AZ3B, C3R1, HNFAG09 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08173, UniProt: Q16581
#2: Chemical ChemComp-A1L6Y / (2S)-5-[bis(azanyl)methylideneamino]-2-[2-(2,2-diphenylethoxy)ethanoylamino]pentanoic acid / SB290157


Mass: 412.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N4O4 / Feature type: SUBJECT OF INVESTIGATION
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: SB290157 bound to human C3aR in complex with Go / Type: COMPLEX / Entity ID: #1 / 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: 47.4 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
12cryoSPARC4.5.3classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 619129 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8I9L

8i9l


Accession code: 8I9L / Source name: PDB / Type: experimental model

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