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- PDB-7rkm: Structure of CX3CL1-US28-Gi-scFv16 in C-state -

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Basic information

Entry
Database: PDB / ID: 7rkm
TitleStructure of CX3CL1-US28-Gi-scFv16 in C-state
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Antibody fragment scFv16
  • Fractalkine
  • G-protein coupled receptor homolog US28
KeywordsMEMBRANE PROTEIN / Viral GPCR / HCMV / cytomegalovirus / G protein complex
Function / homology
Function and homology information


CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of glutamate receptor signaling pathway / autocrine signaling / lymphocyte chemotaxis / synapse pruning / positive regulation of microglial cell migration ...CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of glutamate receptor signaling pathway / autocrine signaling / lymphocyte chemotaxis / synapse pruning / positive regulation of microglial cell migration / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of microglial cell activation / negative regulation of neuron migration / negative regulation of hippocampal neuron apoptotic process / positive regulation of transforming growth factor beta1 production / CCR chemokine receptor binding / microglial cell proliferation / positive regulation of actin filament bundle assembly / leukocyte migration involved in inflammatory response / integrin activation / C-C chemokine receptor activity / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / leukocyte chemotaxis / angiogenesis involved in wound healing / chemokine activity / Chemokine receptors bind chemokines / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / neuron remodeling / symbiont-mediated transformation of host cell / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / macrophage chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / negative regulation of tumor necrosis factor production / negative regulation of cell-substrate adhesion / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / neutrophil chemotaxis / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smooth muscle cell proliferation / cellular response to forskolin / regulation of mitotic spindle organization / negative regulation of cell migration / positive regulation of release of sequestered calcium ion into cytosol / response to ischemia / cell chemotaxis / cell projection / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / microglial cell activation / calcium-mediated signaling / negative regulation of insulin secretion / G protein-coupled receptor binding / defense response / cell-cell adhesion / response to peptide hormone / positive regulation of neuron projection development / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuron cellular homeostasis / regulation of synaptic plasticity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / Olfactory Signaling Pathway / Activation of the phototransduction cascade / integrin binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / cytokine-mediated signaling pathway / positive regulation of angiogenesis / chemotaxis / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / positive regulation of inflammatory response / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / Sensory perception of sweet, bitter, and umami (glutamate) taste
Similarity search - Function
CX3C chemokine domain / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase ...CX3C chemokine domain / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
CHOLESTEROL / 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: 3.5 Å
AuthorsTsutsumi, N. / Qu, Q. / Jude, K.M. / Skiniotis, G. / Garcia, K.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125320 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2022
Title: Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins
Authors: Tsutsumi, N. / Maeda, S. / Qu, Q. / Voegele, M. / Jude, K.M. / Suomivuori, C.M. / Panova, O. / Waghray, D. / Kato, H.E. / Velasco, A. / Dror, R.O. / Skiniotis, G. / Kobilka, B.K. / Garcia, K.C.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
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: Fractalkine
R: G-protein coupled receptor homolog US28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,2267
Polymers164,8406
Non-polymers3871
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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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 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40283.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63096
#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 Fractalkine / C-X3-C motif chemokine 1 / CX3C membrane-anchored chemokine / Neurotactin / Small-inducible cytokine D1


Mass: 10013.487 Da / Num. of mol.: 1 / Fragment: UNP residues 25-101
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
Source: (gene. exp.) Human betaherpesvirus 5 / 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: Trichoplusia ni (cabbage looper)
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has ligand of interestN
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-US28-Gi-scFv16 complexCOMPLEX#1-#60MULTIPLE SOURCES
2Gi heterotrimerCOMPLEX#1-#31RECOMBINANT
3scFv16COMPLEX#41RECOMBINANT
4CX3CL1-US28COMPLEX#5-#61RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
120.09 MDaNO
230.03 MDaNO
340.05 MDa
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular location
12Homo sapiens (human)9606Membrane
23Mus musculus (house mouse)10090
34Human betaherpesvirus 59606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)9606
23Trichoplusia ni (cabbage looper)7111
34Homo sapiens (human)9606
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
50.05 % w/vOctyl beta-D-glucopyranoside1
SpecimenConc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: 1 s blotting before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Calibrated magnification: 60976 X / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 83 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4546
Details: The same specimen/movie data as the OC-state CX3CL1-US28-Gi-scFv16 (7RKM).
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.06CTF correction
5RELION3.1CTF correction
10PHENIXmodel refinement
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionDetails: Final per-particle CTF values were determined by Relion 3.1 CTF correction.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1348802
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143691 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059697
ELECTRON MICROSCOPYf_angle_d0.96113144
ELECTRON MICROSCOPYf_dihedral_angle_d5.0381316
ELECTRON MICROSCOPYf_chiral_restr0.0581493
ELECTRON MICROSCOPYf_plane_restr0.0051654

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