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- EMDB-62600: Structure of SB290157 bound to human C3aR in complex with Go (Rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-62600
TitleStructure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)
Map data
Sample
  • Complex: SB290157 bound to human C3aR in complex with Go
    • Protein or peptide: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
  • Ligand: (2S)-5-[bis(azanyl)methylideneamino]-2-[2-(2,2-diphenylethoxy)ethanoylamino]pentanoic acid
KeywordsG protein coupled receptor / G protein / Membrane protein / Immunite system / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsBanerjee R / Sano FK / Yadav MK / Sawada K / Ganguly M / Mishra S / Dalal A / Nureki O / Shukla AK
Funding support United Kingdom, India, 3 items
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 FK / Yadav MK / Sawada K / Ganguly M / Mishra S / Dalal A / Nureki O / Shukla AK
History
DepositionDec 5, 2024-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62600.png

Downloads & links

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Map

FileDownload / File: emd_62600.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 232.408 Å		1.06 Å/pix.
x 220 pix.
= 232.408 Å		1.06 Å/pix.
x 220 pix.
= 232.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0564 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.028158046 - 1.9348577
Average (Standard dev.)0.0013049992 (±0.021947915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 232.40799 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62600_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_62600_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 : SB290157 bound to human C3aR in complex with Go

EntireName: SB290157 bound to human C3aR in complex with Go
Components
  • Complex: SB290157 bound to human C3aR in complex with Go
    • Protein or peptide: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
  • Ligand: (2S)-5-[bis(azanyl)methylideneamino]-2-[2-(2,2-diphenylethoxy)ethanoylamino]pentanoic acid

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Supramolecule #1: SB290157 bound to human C3aR in complex with Go

SupramoleculeName: SB290157 bound to human C3aR in complex with Go / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotacti...

MacromoleculeName: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.808422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSASF SAETNSTDLL SQPWNEPPVI LSMVILSLT FLLGLPGNGL VLWVAGLKMQ RTVNTIWFLH LTLADLLCCL SLPFSLAHLA LQGQWPYGRF LCKLIPSIIV L NMFASVFL ...String:
MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSASF SAETNSTDLL SQPWNEPPVI LSMVILSLT FLLGLPGNGL VLWVAGLKMQ RTVNTIWFLH LTLADLLCCL SLPFSLAHLA LQGQWPYGRF LCKLIPSIIV L NMFASVFL LTAISLDRCL VVFKPIWCQN HRNVGMACSI CGCIWVVAFV MCIPVFVYRE IFTTDNHNRC GYKFGLSSSL DY PDFYGDP LENRSLENIV QPPGEMNDRL DPSSFQTNDH PWTVPTVFQP QTFQRPSADS LPRGSARLTS QNLYSNVFKP ADV VSPKIP SGFPIEDHET SPLDNSDAFL STHLKLFPSA SSNSFYESEL PQGFQDYYNL GQFTDDDQVP TPLVAITITR LVVG FLLPS VIMIACYSFI VFRMQRGRFA KSQSKTFRVA VVVVAVFLVC WTPYHIFGVL SLLTDPETPL GKTLMSWDHV CIALA SANS CFNPFLYALL GKDFRKKARQ SIQGILEAAF SEELTRSTHC PSNNVISERN STTV

UniProtKB: Muscarinic acetylcholine receptor M4, C3a anaphylatoxin chemotactic receptor

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Macromolecule #2: (2S)-5-[bis(azanyl)methylideneamino]-2-[2-(2,2-diphenylethoxy)eth...

MacromoleculeName: (2S)-5-[bis(azanyl)methylideneamino]-2-[2-(2,2-diphenylethoxy)ethanoylamino]pentanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1L6Y
Molecular weightTheoretical: 412.482 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8i9l

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 619129
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8i9l


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9kvs:
Structure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)

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