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- EMDB-66930: Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C'-state wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-66930
TitleStructure of the CX3CL1.44-US28-GqiN18-scFv16 in the C'-state with AHD visible
Map datauniformly sharpened map
Sample
  • Complex: CX3CL1.44-US28-GqiN18-scFv16
    • Complex: Gq heterotrimer
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: CX3CL1.44-US28
      • Protein or peptide: Processed fractalkine
      • Protein or peptide: G-protein coupled receptor homolog US28
    • Complex: scFv16
      • Protein or peptide: antibody fragment scFv16
KeywordsMEMBRANE PROTEIN / GPCR / active-like state / 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
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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsJude KM / Garcia KC / Tsutsumi N
Funding support Japan, 1 items
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 KM / Garcia KC / Tsutsumi N
History
DepositionNov 4, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66930.png

Downloads & links

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Map

FileDownload / File: emd_66930.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationuniformly sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 300 pix.
= 305.4 Å		1.02 Å/pix.
x 300 pix.
= 305.4 Å		1.02 Å/pix.
x 300 pix.
= 305.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.018 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0723
Minimum - Maximum-0.56045973 - 0.8420111
Average (Standard dev.)-0.000080855716 (±0.013640707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 305.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMHancer-sharpened map

Fileemd_66930_additional_1.map
AnnotationDeepEMHancer-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66930_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66930_half_map_2.map
Projections & Slices
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Sample components

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Entire : CX3CL1.44-US28-GqiN18-scFv16

EntireName: CX3CL1.44-US28-GqiN18-scFv16
Components
  • Complex: CX3CL1.44-US28-GqiN18-scFv16
    • Complex: Gq heterotrimer
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: CX3CL1.44-US28
      • Protein or peptide: Processed fractalkine
      • Protein or peptide: G-protein coupled receptor homolog US28
    • Complex: scFv16
      • Protein or peptide: antibody fragment scFv16

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Supramolecule #1: CX3CL1.44-US28-GqiN18-scFv16

SupramoleculeName: CX3CL1.44-US28-GqiN18-scFv16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: Gq heterotrimer

SupramoleculeName: Gq heterotrimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Supramolecule #3: CX3CL1.44-US28

SupramoleculeName: CX3CL1.44-US28 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Details: Complex between chemokine analog CX3CL1.44 and HCMV GPCR US28
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Details: GPCR/G protein complex-stabilizing antibody fragment scFv16
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 30 KDa

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Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine n...

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
type: protein_or_peptide / ID: 1
Details: residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI
Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.249934 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GCTLSAEDKA AVERSKMIER QLRRDKRDAR RELKLLLLGT GESGKSTFIK QMRIIHGSGY SDEDKRGFTK LVYQNIFTAM QAMIRAMDT LKIPYKYEHN KAHAQLVREV DVEKVSAFEN PYVDAIKSLW NDPGIQECYD RRREYQLSDS TKYYLNDLDR V ADPAYLPT ...String:
GCTLSAEDKA AVERSKMIER QLRRDKRDAR RELKLLLLGT GESGKSTFIK QMRIIHGSGY SDEDKRGFTK LVYQNIFTAM QAMIRAMDT LKIPYKYEHN KAHAQLVREV DVEKVSAFEN PYVDAIKSLW NDPGIQECYD RRREYQLSDS TKYYLNDLDR V ADPAYLPT QQDVLRVRVP TTGIIEYPFD LQSVIFRMVD VGGQRSERRK WIHCFENVTS IMFLVALSEY DQVLVESDNE NR MEESKAL FRTIITYPWF QNSSVILFLN KKDLLEEKIM YSHLVDYFPE YDGPQRDAQA AREFILKMFV DLNPDSDKII YSH FTCATD TENIRFVFAA VKDTILQLNL KEYNLV

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.728152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.432554 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFC

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: antibody fragment scFv16

MacromoleculeName: antibody fragment scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.340482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGSLEVLFQ

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Macromolecule #5: Processed fractalkine

MacromoleculeName: Processed fractalkine / type: protein_or_peptide / ID: 5 / Details: residues 1-7 QHHGVTK replaced with VRPHINN / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.072578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VRPHINNCNI TCSKMTSKIP VALLIHYQQN QASCGKRAII LETRQHRLFC ADPKEQWVKD AMQHLDRQAA ALTRNGGSGS GSAAALEVL FQ

UniProtKB: Fractalkine

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Macromolecule #6: G-protein coupled receptor homolog US28

MacromoleculeName: G-protein coupled receptor homolog US28 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 42.041098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDAMT PTTTTAELTT EFDYDEDATP CVFTDVLNQS KPVTLFLYGV VFLFGSIGNF LVIFTITWRR RIQCSGDVYF INLAAADLL FVCTLPLWMQ YLLDHNSLAS VPCTLLTACF YVAMFASLCF ITEIALDRYY AIVYMRYRPV KQACLFSIFW W IFAVIIAI ...String:
DYKDDDDAMT PTTTTAELTT EFDYDEDATP CVFTDVLNQS KPVTLFLYGV VFLFGSIGNF LVIFTITWRR RIQCSGDVYF INLAAADLL FVCTLPLWMQ YLLDHNSLAS VPCTLLTACF YVAMFASLCF ITEIALDRYY AIVYMRYRPV KQACLFSIFW W IFAVIIAI PHFMVVTKKD NQCMTDYDYL EVSYPIILNV ELMLGAFVIP LSVISYCYYR ISRIVAVSQS RHKGRIVRVL IA VVLVFII FWLPYHLTLF VDTLKLLKWI SSSCEFERSL KRALILTESL AFCHCCLNPL LYVFVGTKFR QELHCLLAEF RQR LFSRDV SWYHSMSFSR RSSPSRRETS SDTLSDEVCR VSQIIP

UniProtKB: G protein-coupled receptor homolog US28

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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

Concentration20 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
10.0 mMHepes-sodium salt
150.0 mMSodium chloride
0.001 % w/vLauryl Maltose Neopentyl Glycol
0.001 % w/vGlyco-diosgenin
0.0001 % w/vCholesterol Hydrogen Succinate
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: LEICA EM GP / Details: 3 s blotting before plunging.
Detailschemokine-GPCR complex coupled to Gq heterotrimer

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 11773 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 57624 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 8400483 / Details: initial particles that appeared to be protein
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6)
Details: CryoSPARC patch CTF estimation and global/local CTF refinements
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio reconstruction model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 69523
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Details: CryoSPARC ab-initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Details: CryoSPARC non-uniform local refinement
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9xj7:
Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C'-state with AHD visible

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