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- PDB-8zwf: cryoEM structure of JR14a bound C3aR-BRIL-BAG2 complex -

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Basic information

Entry
Database: PDB / ID: 8zwf
TitlecryoEM structure of JR14a bound C3aR-BRIL-BAG2 complex
Components
  • Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
  • anti-BRIL Fab HC
  • anti-BRIL Fab LC
KeywordsIMMUNE SYSTEM / complement receptor / C3aR / Non-peptide agonist / JR14a
Function / homology
Function and homology information


complement component C3a receptor activity / complement component C5a receptor activity / complement receptor mediated signaling pathway / positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / positive regulation of neutrophil chemotaxis / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...complement component C3a receptor activity / complement component C5a receptor activity / complement receptor mediated signaling pathway / positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / positive regulation of neutrophil chemotaxis / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / blood circulation / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / azurophil granule membrane / endosome to lysosome transport / response to psychosocial stress / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of macrophage chemotaxis / positive regulation of cAMP/PKA signal transduction / positive regulation of vascular endothelial growth factor production / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / neuronal dense core vesicle / brown fat cell differentiation / Purinergic signaling in leishmaniasis infection / specific granule membrane / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / receptor-mediated endocytosis / response to cold / Peptide ligand-binding receptors / Regulation of Complement cascade / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / positive regulation of angiogenesis / chemotaxis / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / microtubule cytoskeleton / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription by RNA polymerase II / early endosome / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / lysosome / receptor complex / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / cilium / ciliary basal body / apical plasma membrane / G protein-coupled receptor signaling pathway / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
C3a anaphylatoxin chemotactic receptor / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Beta 2 adrenoceptor / Adrenoceptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...C3a anaphylatoxin chemotactic receptor / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Beta 2 adrenoceptor / Adrenoceptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / Beta-2 adrenergic receptor / Soluble cytochrome b562 / C3a anaphylatoxin chemotactic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLuo, P. / Xu, Y. / Xu, H.E.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82121005 China
National Natural Science Foundation of China (NSFC)32130022 China
CitationJournal: Cell Discov / Year: 2025
Title: Structural insights into the agonist activity of the nonpeptide modulator JR14a on C3aR.
Authors: Ping Luo / Wenwen Xin / Shimeng Guo / Xin Li / Qing Zhang / Youwei Xu / Xinheng He / Yue Wang / Wenjia Fan / Qingning Yuan / Kai Wu / Wen Hu / Youwen Zhuang / H Eric Xu / Xin Xie /
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
C: anti-BRIL Fab LC
D: anti-BRIL Fab HC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0234
Polymers122,4903
Non-polymers5331
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 Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562 / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / C3AR / C3a-R / Cytochrome b-562


Mass: 72253.016 Da / Num. of mol.: 1 / Mutation: E27Q,M29W,H124I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADRB2, ADRB2R, B2AR, C3AR1, AZ3B, C3R1, HNFAG09, cybC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P07550, UniProt: Q16581, UniProt: P0ABE7
#2: Antibody anti-BRIL Fab LC


Mass: 25915.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody anti-BRIL Fab HC


Mass: 24321.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-A1D9A / (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid / JR14a


Mass: 533.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26Cl2N4O3S / 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: JR14a bound C3aR-BRIL-BAG2 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.3
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150052 / Symmetry type: POINT

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