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- PDB-4xt3: Structure of a viral GPCR bound to human chemokine CX3CL1 -

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Basic information

Entry
Database: PDB / ID: 4xt3
TitleStructure of a viral GPCR bound to human chemokine CX3CL1
Components
  • Fractalkine
  • G-protein coupled receptor homolog US28
KeywordsVIRAL PROTEIN/SIGNALLING PROTEIN / GPCR / chemokine / membrane protein / complex / VIRAL PROTEIN-CYTOKINE complex / VIRAL PROTEIN-SIGNALLING 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 hippocampal neuron apoptotic process / negative regulation of glutamate receptor signaling pathway / autocrine signaling / lymphocyte chemotaxis / synapse pruning ...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 hippocampal neuron apoptotic process / 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 / 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 / C-C chemokine receptor activity / integrin activation / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / 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 / positive regulation of neuroblast proliferation / symbiont-mediated transformation of host cell / positive chemotaxis / chemoattractant activity / macrophage chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / regulation of neurogenesis / negative regulation of tumor necrosis factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of cell-substrate adhesion / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of cell migration / response to ischemia / cell projection / cell chemotaxis / positive regulation of smooth muscle cell proliferation / microglial cell activation / calcium-mediated signaling / defense response / cytokine-mediated signaling pathway / cell-cell adhesion / regulation of synaptic plasticity / positive regulation of neuron projection development / neuron cellular homeostasis / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of angiogenesis / chemotaxis / integrin binding / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / neuron projection / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / host cell plasma membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Rhopdopsin 7-helix transmembrane proteins ...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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
triacetyl-beta-chitotriose / PHOSPHATE ION / Unknown ligand / G-protein coupled receptor homolog US28 / Fractalkine
Similarity search - Component
Biological speciesCytomegalovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.801 Å
AuthorsBurg, J.S. / Jude, K.M. / Waghray, D. / Garcia, K.C.
CitationJournal: Science / Year: 2015
Title: Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.
Authors: Burg, J.S. / Ingram, J.R. / Venkatakrishnan, A.J. / Jude, K.M. / Dukkipati, A. / Feinberg, E.N. / Angelini, A. / Waghray, D. / Dror, R.O. / Ploegh, H.L. / Garcia, K.C.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_name_com / entity_poly / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_conn / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.type / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.entity_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G-protein coupled receptor homolog US28
B: Fractalkine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8725
Polymers52,0552
Non-polymers8183
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-7 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 192.700, 94.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

PO4

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Components

#1: 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.) Cytomegalovirus / Cell line (production host): HEK293s GnTI- / Production host: Homo sapiens (human) / References: UniProt: P69332
#2: 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 / Cell line (production host): HEK293s GnTI- / Production host: Homo sapiens (human) / References: UniProt: P78423
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 26

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.4 / Details: PEG 300, HEPES, ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.8→48.92 Å / Num. obs: 4834 / % possible obs: 85 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.275 / Net I/σ(I): 4.1
Reflection shellResolution: 3.8→3.937 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.6 / % possible all: 55.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS, 1F2L, 3ONA

4mbs

1f2l

3ona


Resolution: 3.801→48.92 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3221 484 10.03 %random selection
Rwork0.2835 ---
obs0.2878 4827 84.94 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.801→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 56 0 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032851
X-RAY DIFFRACTIONf_angle_d0.8743912
X-RAY DIFFRACTIONf_dihedral_angle_d11.365942
X-RAY DIFFRACTIONf_chiral_restr0.031483
X-RAY DIFFRACTIONf_plane_restr0.005468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8006-4.35030.36541200.30131079X-RAY DIFFRACTION64
4.3503-5.47980.34581740.30541571X-RAY DIFFRACTION94
5.4798-48.92430.29141900.26361693X-RAY DIFFRACTION96

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