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- EMDB-60525: cryoEM structure of JR14a bound C3aR-BRIL-BAG2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60525
TitlecryoEM structure of JR14a bound C3aR-BRIL-BAG2 complex
Map data
Sample
  • Complex: JR14a bound C3aR-BRIL-BAG2 complex
    • Protein or peptide: Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab LC
    • Protein or peptide: anti-BRIL Fab HC
  • Ligand: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid
Keywordscomplement receptor / C3aR / Non-peptide agonist / JR14a / IMMUNE SYSTEM
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 / norepinephrine binding / heat generation / Adrenoceptors / blood circulation / positive regulation of lipophagy / azurophil granule membrane / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / endosome to lysosome transport / response to psychosocial stress / diet induced thermogenesis / positive regulation of macrophage chemotaxis / neuronal dense core vesicle / 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 / 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 / positive regulation of angiogenesis / cellular response to amyloid-beta / chemotaxis / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / positive regulation of cytosolic calcium ion concentration / microtubule cytoskeleton / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription by RNA polymerase II / periplasmic space / early endosome / lysosome / electron transfer activity / cell surface receptor signaling pathway / receptor complex / endosome / positive regulation of MAPK cascade / endosome membrane / Ub-specific processing proteases / ciliary basal body / cilium / G protein-coupled receptor signaling pathway / apical plasma membrane / inflammatory response / iron ion binding / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLuo P / Xu Y / Xu HE
Funding support China, 2 items
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, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60525.png

Downloads & links

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Map

FileDownload / File: emd_60525.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.023137579 - 0.055358503
Average (Standard dev.)0.000050014758 (±0.00089846924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60525_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60525_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : JR14a bound C3aR-BRIL-BAG2 complex

EntireName: JR14a bound C3aR-BRIL-BAG2 complex
Components
  • Complex: JR14a bound C3aR-BRIL-BAG2 complex
    • Protein or peptide: Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab LC
    • Protein or peptide: anti-BRIL Fab HC
  • Ligand: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid

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Supramolecule #1: JR14a bound C3aR-BRIL-BAG2 complex

SupramoleculeName: JR14a bound C3aR-BRIL-BAG2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor...

MacromoleculeName: Beta-2 adrenergic receptor,C3a anaphylatoxin chemotactic receptor,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.253016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDVDM GQPGNGSAFL LAPNGSHAPD HDVTQQRDEE NLYFQGASMA SFSAETNSTD LLSQPWNEPP VILSMVILSL TFLLGLPGN GLVLWVAGLK MQRTVNTIWF LHLTLADLLC CLSLPFSLAH LALQGQWPYG RFLCKLIPSI IVLNMFASVF L LTAISLDR ...String:
DYKDDDDVDM GQPGNGSAFL LAPNGSHAPD HDVTQQRDEE NLYFQGASMA SFSAETNSTD LLSQPWNEPP VILSMVILSL TFLLGLPGN GLVLWVAGLK MQRTVNTIWF LHLTLADLLC CLSLPFSLAH LALQGQWPYG RFLCKLIPSI IVLNMFASVF L LTAISLDR CLVVFKPIWC QNHRNVGMAC SICGCIWVVA FVMCIPVFVY REIFTTDNHN RCGYKFGLSS SLDYPDFYGD PL ENRSLEN IVQPPGEMND RLDPSSFQTN DHPWTVPTVF QPQTFQRPSA DSLPRGSARL TSQNLYSNVF KPADVVSPKI PSG FPIEDH ETSPLDNSDA FLSTHLKLFP SASSNSFYES ELPQGFQDYY NLGQFTDDDQ VPTPLVAITI TRLVVGFLLP SVIM IACYS FIVFRARRQL ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGF DILV GQIDDALKLA NEGKVKEAQA AAEQLKTTRN AYIQKYLERA RSTLSKTFRV AVVVVAVFLV CWTPYHIFGV LSLLTD PET PLGKTLMSWD HVCIALASAN SCFNPFLYAL LGKDFRKKAR QSIQGILEAA FSEELTRSTH CPSNNVISER NSTTVHH HH HHHH

UniProtKB: Beta-2 adrenergic receptor, C3a anaphylatoxin chemotactic receptor, Soluble cytochrome b562, C3a anaphylatoxin chemotactic receptor

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Macromolecule #2: anti-BRIL Fab LC

MacromoleculeName: anti-BRIL Fab LC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.91566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGECVD ENLYFQGASH HHHHHHH

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Macromolecule #3: anti-BRIL Fab HC

MacromoleculeName: anti-BRIL Fab HC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.321084 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK S

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Macromolecule #4: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl...

MacromoleculeName: (2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1D9A
Molecular weightTheoretical: 533.47 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150052
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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