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- PDB-9xjp: Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state, che... -

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Basic information

Entry
Database: PDB / ID: 9xjp
TitleStructure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state, chemokine domain fully modeled
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Antibody fragment scFv16
  • G-protein coupled receptor homolog US28
  • Processed fractalkine
KeywordsMEMBRANE PROTEIN / GPCR / intermediate state / GDP / engineered chemokine / HCMV / viral protein / viral-host interaction
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 / microglial cell proliferation / negative regulation of hippocampal neuron apoptotic process / 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 / leukocyte migration involved in inflammatory response / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / 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 / C-C chemokine binding / eosinophil chemotaxis / C-C chemokine receptor activity / 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 / neuron remodeling / negative regulation of interleukin-6 production / positive chemotaxis / chemoattractant activity / cell projection / 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 / regulation of eating behavior / adenylate cyclase inhibitor activity / T cell migration / positive regulation of protein localization to cell cortex / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / positive regulation of smooth muscle cell proliferation / D2 dopamine receptor binding / adenylate cyclase-inhibiting dopamine receptor signaling pathway / GTPase activator activity / negative regulation of cell migration / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / regulation of G protein-coupled receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / cellular response to forskolin / regulation of mitotic spindle organization / mast cell degranulation / chemokine-mediated signaling pathway / calcium-mediated signaling / positive regulation of neuron projection development / cell chemotaxis / establishment of mitotic spindle orientation / defense response / cell-cell adhesion / neuropeptide signaling pathway / Regulation of insulin secretion / response to prostaglandin E / microglial cell activation / regulation of synaptic plasticity / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / integrin binding / blood coagulation / chemotaxis / response to peptide hormone / cytokine-mediated signaling pathway / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of inflammatory response
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, group I ...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, group I / 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
CHOLESTEROL / 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 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / G protein-coupled receptor homolog US28 / Fractalkine
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Human betaherpesvirus 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsJude, K.M. / Garcia, K.C. / 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. / Garcia, K.C. / Tsutsumi, N.
History
DepositionNov 5, 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
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
R: G-protein coupled receptor homolog US28
L: Processed fractalkine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,0819
Polymers165,8656
Non-polymers1,2173
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
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 / Adenylate cyclase-inhibiting G alpha protein / 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 from G(i),residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI from G(i)
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAQ, GAQ / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P63096, 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 RL

#5: 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.) Human betaherpesvirus 5 / Gene: US28 / Production host: Homo sapiens (human) / References: UniProt: P69332
#6: Protein Processed fractalkine / engineered fractalkine CX3CL1.44


Mass: 10072.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-7 QHHGVTK replaced with VRPHINN / Source: (gene. exp.) Homo sapiens (human) / Gene: CX3CL1, FKN, NTT, SCYD1, A-152E5.2 / Production host: Homo sapiens (human) / References: UniProt: P78423

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Antibody , 1 types, 1 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)

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Non-polymers , 2 types, 3 molecules

#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
#8: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O

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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-IDSourceDetails (eV)
1CX3CL1.44-US28-GqiN18-scFv16COMPLEX#1-#60MULTIPLE SOURCES
2Gq heterotrimerCOMPLEX#1-#31RECOMBINANT
3CX3CL1.44-US28COMPLEX#5-#61RECOMBINANTComplex between chemokine analog CX3CL1.44 and HCMV GPCR US28
4scFv16COMPLEX#41RECOMBINANTGPCR/G protein complex-stabilizing antibody fragment scFv16
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.18 MDaNO
220.1 MDaNO
310.05 MDaNO
440.03 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Trichoplusia ni (cabbage looper)7111
22Trichoplusia ni (cabbage looper)7111
33Homo sapiens (human)9606
44Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 7.2
Buffer component
IDConc.NameBuffer-ID
110 mMHepes-sodium salt1
2150 mMSodium chloride1
30.001 % w/vLauryl Maltose Neopentyl Glycol1
40.001 % w/vGlyco-diosgenin1
50.0001 % w/vCholesterol Hydrogen Succinate1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: chemokine-GPCR complex coupled to Gq heterotrimer
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 289 K / Details: 3 s blotting before plunging

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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 / Calibrated magnification: 57624 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 2 / Num. of real images: 11773
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
4cryoSPARC4.6CTF correction
7PHENIXmodel fitting
9cryoSPARC4.6initial Euler assignment
10cryoSPARC4.6final Euler assignment
11cryoSPARC4.6classification
12cryoSPARC4.63D reconstruction
13PHENIX1.21.2_5419model refinement
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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64658 / 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-IDAccession codeChain-IDInitial refinement model-IDSource nameType
17rkf

7rkf

B7rkfB1PDBexperimental model
2AAlphaFoldin silico model
37rkf

7rkf

C7rkfC1PDBexperimental model
47rkf

7rkf

D7rkfD1PDBexperimental model
54xt1

4xt1

R4xt1R3PDBexperimental model
64xt1

4xt1

L4xt1L3PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002710939
ELECTRON MICROSCOPYf_angle_d0.490214854
ELECTRON MICROSCOPYf_chiral_restr0.04091682
ELECTRON MICROSCOPYf_plane_restr0.00361870
ELECTRON MICROSCOPYf_dihedral_angle_d5.36151623

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