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- PDB-9xiy: Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state -

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Basic information

Entry
Database: PDB / ID: 9xiy
TitleStructure of the CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • G-protein coupled receptor homolog US28
  • Processed fractalkine
  • antibody fragment scFv16
KeywordsSIGNALING PROTEIN / GPCR / G protein
Function / homology
Function and homology information


CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / negative regulation of neuron migration / positive regulation of microglial cell migration / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of microglial cell activation ...CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / negative regulation of neuron migration / positive regulation of microglial cell migration / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of microglial cell activation / negative regulation of hippocampal neuron apoptotic process / microglial cell proliferation / positive regulation of gonadotropin secretion / autocrine signaling / phospholipase C-activating tachykinin receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / CCR chemokine receptor binding / chemokine receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / leukocyte migration involved in inflammatory response / positive regulation of actin filament bundle assembly / regulation of platelet activation / synapse pruning / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / entrainment of circadian clock / sensory perception of itch / positive regulation of membrane depolarization / integrin activation / phototransduction, visible light / eosinophil chemotaxis / positive regulation of cell-matrix adhesion / neuron cellular homeostasis / positive regulation of neuroblast proliferation / chemokine activity / leukocyte chemotaxis / Chemokine receptors bind chemokines / regulation of canonical Wnt signaling pathway / negative regulation of interleukin-1 beta production / symbiont-mediated transformation of host cell / cell projection / neuron remodeling / negative regulation of interleukin-6 production / positive chemotaxis / chemoattractant activity / glutamate receptor signaling pathway / negative regulation of apoptotic signaling pathway / negative regulation of cell-substrate adhesion / negative regulation of tumor necrosis factor production / regulation of neurogenesis / postsynaptic cytosol / photoreceptor outer segment / response to ischemia / hormone-mediated signaling pathway / cellular response to acidic pH / symbiont-mediated perturbation of host defense response / positive regulation of smooth muscle cell proliferation / GTPase activator activity / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of release of sequestered calcium ion into cytosol / mast cell degranulation / chemokine-mediated signaling pathway / positive regulation of neuron projection development / defense response / cell chemotaxis / cell-cell adhesion / neuropeptide signaling pathway / microglial cell activation / response to prostaglandin E / regulation of synaptic plasticity / chemotaxis / G protein-coupled receptor binding / integrin binding / blood coagulation / cytokine-mediated signaling pathway / G-protein beta/gamma-subunit complex binding / positive regulation of inflammatory response / Olfactory Signaling Pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / glucose homeostasis / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion
Similarity search - Function
CX3C chemokine domain / G-protein alpha subunit, group Q / Chemokine receptor family / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / : / G protein alpha subunit, helical insertion ...CX3C chemokine domain / G-protein alpha subunit, group Q / Chemokine receptor family / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / : / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / G-protein, beta subunit / 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. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / G protein-coupled receptor homolog US28 / Fractalkine
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Cytomegalovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJude, K.M. / Tsutsumi, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01965 Japan
CitationJournal: To Be Published
Title: Structural basis of a stepwise Gq activation by a chemokine receptor US28
Authors: Jude, K.M. / Tsutsumi, N.
History
DepositionNov 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha,Guanine nucleotide-binding protein G(q) subunit alpha
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D: antibody fragment scFv16
L: Processed fractalkine
R: G-protein coupled receptor homolog US28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,3087
Polymers165,8656
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABC

#1: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha,Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein alpha-q


Mass: 41249.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 ...Details: residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAQ, GAQ / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P50148, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37728.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7432.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768

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Protein , 2 types, 2 molecules LR

#5: Protein Processed fractalkine


Mass: 10072.578 Da / Num. of mol.: 1 / Mutation: residues 1-7 QHHGVTK replaced with VRPHINN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CX3CL1, FKN, NTT, SCYD1, A-152E5.2 / Production host: Homo sapiens (human) / References: UniProt: P78423
#6: Protein G-protein coupled receptor homolog US28 / HHRF3


Mass: 42041.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-9 DYKDDDDA are a FLAG tag / Source: (gene. exp.) Cytomegalovirus / Gene: US28 / Production host: Homo sapiens (human) / References: UniProt: P69332

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Antibody / Non-polymers , 2 types, 2 molecules D

#4: Antibody antibody fragment scFv16


Mass: 27340.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

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Details

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

Component
IDNameTypeEntity IDParent-IDSource
1CX3CL1.44-activated us28 bound to Gq trimer with scFv fiducialCOMPLEX#1-#60MULTIPLE SOURCES
2Gq trimerCOMPLEX#1-#31RECOMBINANT
3CX3CL1.44-US28COMPLEX#5-#61RECOMBINANT
4scFv16COMPLEX#41RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.165594 MDaNO
21NO
31NO
41NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Trichoplusia ni (cabbage looper)7111
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
10.01 MHEPES1
2.15 Msodium chlorideNaCl1
3.005 %lauryl maltose neopentyl glycol1
4.0005 %cholesterol hemisuccinate1
510 mMCHAPSO1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 289 K

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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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11773
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2PHENIX2.0_5936model refinement
5cryoSPARC4.6CTF correction
10cryoSPARC4.6initial Euler assignment
11cryoSPARC4.6final Euler assignment
12cryoSPARC4.6classification
13cryoSPARC4.63D reconstruction
CTF correctionDetails: CryoSPARC patch CTF estimation and global/local CTF refinements
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8400483 / Details: initial particles that appeared to be protein
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70394 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDChain-IDSource nameTypeAccession codeInitial refinement model-ID
1AAlphaFoldin silico model
27RKF

7rkf

BBPDBexperimental model7RKF2
37RKF

7rkf

CCPDBexperimental model7RKF2
47RKF

7rkf

DDPDBexperimental model7RKF2
54XT1

4xt1

LLPDBexperimental model4XT13
64XT1

4xt1

RRPDBexperimental model4XT13
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 109.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002510229
ELECTRON MICROSCOPYf_angle_d0.46913877
ELECTRON MICROSCOPYf_chiral_restr0.04041566
ELECTRON MICROSCOPYf_plane_restr0.00351749
ELECTRON MICROSCOPYf_dihedral_angle_d11.58033686

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