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- PDB-3ona: The SECRET domain in complex with CX3CL1 -

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Basic information

Entry
Database: PDB / ID: 3ona
TitleThe SECRET domain in complex with CX3CL1
Components
  • CX3CL1 protein
  • Tumour necrosis factor receptor
KeywordsVIRAL PROTEIN/CYTOKINE / beta-sandwich / chemokine fold / vTNFR-chemokine complex / VIRAL PROTEIN-CYTOKINE 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 / tumor necrosis factor receptor activity ...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 / tumor necrosis factor receptor activity / 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 / tumor necrosis factor binding / CCR chemokine receptor binding / microglial cell proliferation / positive regulation of actin filament bundle assembly / leukocyte migration involved in inflammatory response / integrin activation / chemokine-mediated signaling pathway / eosinophil chemotaxis / leukocyte chemotaxis / angiogenesis involved in wound healing / positive regulation of membrane protein ectodomain proteolysis / 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 / positive chemotaxis / chemoattractant activity / macrophage chemotaxis / negative regulation of interleukin-6 production / regulation of T cell proliferation / 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 / 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 / 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 / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Viral Chemokine Inhibitor; Chain A - #20 / Poxvirus, TNF receptor-II, C-terminal / Poxvirus, TNF-alpha receptor-II / Tumour necrosis factor receptor, SECRET domain / Tumor necrosis factor receptor, N-terminal, viral / Viral Chemokine Inhibitor; Chain A / : / CX3C chemokine domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region ...Viral Chemokine Inhibitor; Chain A - #20 / Poxvirus, TNF receptor-II, C-terminal / Poxvirus, TNF-alpha receptor-II / Tumour necrosis factor receptor, SECRET domain / Tumor necrosis factor receptor, N-terminal, viral / Viral Chemokine Inhibitor; Chain A / : / CX3C chemokine domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fractalkine / CX3CL1 protein / Tumour necrosis factor receptor
Similarity search - Component
Biological speciesEctromelia virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, X.Q. / Xue, X.G. / Wang, D.L.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structural basis of chemokine sequestration by CrmD, a poxvirus-encoded tumor necrosis factor receptor
Authors: Xue, X.G. / Lu, Q.Y. / Wei, H. / Wang, D.L. / Chen, D.W. / He, G.J. / Huang, L. / Wang, H.Z. / Wang, X.Q.
History
DepositionAug 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 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: Tumour necrosis factor receptor
B: CX3CL1 protein


Theoretical massNumber of molelcules
Total (without water)26,9832
Polymers26,9832
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-4 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.330, 71.330, 93.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-81-

HOH

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Components

#1: Protein Tumour necrosis factor receptor


Mass: 18012.010 Da / Num. of mol.: 1 / Fragment: SECRET domain, UNP residues 162-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Gene: crmD / Production host: Escherichia coli (E. coli) / References: UniProt: Q7TDW8
#2: Protein CX3CL1 protein / CX3CL1


Mass: 8971.408 Da / Num. of mol.: 1 / Fragment: chemokine domain, UNP residues 24-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6I9S9, UniProt: P78423*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Li2SO4, 0.1M Tris.Cl, 20% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 8839 / Num. obs: 8847 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3ON9 AND 1F2L

3on9

1f2l


Resolution: 2.6→29.317 Å / SU ML: 1.79 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 393 4.76 %random
Rwork0.1961 ---
obs0.1986 8262 93.62 %-
all-8847 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.036 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.022 Å20 Å2-0 Å2
2---1.022 Å20 Å2
3----17.754 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 0 28 1772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011779
X-RAY DIFFRACTIONf_angle_d1.2822413
X-RAY DIFFRACTIONf_dihedral_angle_d18.876634
X-RAY DIFFRACTIONf_chiral_restr0.076289
X-RAY DIFFRACTIONf_plane_restr0.004307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5974-2.9730.37161130.27832349X-RAY DIFFRACTION85
2.973-3.74440.29521350.20262646X-RAY DIFFRACTION96
3.7444-29.31870.20721450.1732874X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.50160.4653-0.36414.08540.39863.6319-0.12930.24830.1148-0.0680.13380.3761-0.2636-0.833300.6583-0.08740.01070.6687-0.08790.612219.0029-12.95676.5494
22.666-0.2411-1.12543.52691.16132.2269-0.2488-0.4634-0.01421.16930.0966-0.3473-0.11960.65530.00010.7071-0.099-0.02250.72670.03370.657934.993-26.7368-4.2512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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