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- PDB-3fpu: The crystallographic structure of the Complex between Evasin-1 an... -

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Basic information

Entry
Database: PDB / ID: 3fpu
TitleThe crystallographic structure of the Complex between Evasin-1 and CCL3
Components
  • C-C motif chemokine 3
  • Evasin-1
KeywordsIMMUNE SYSTEM / protein:protein complex / chemokine / Glycoprotein / Secreted / Chemotaxis / Cytokine / Inflammatory response
Function / homology
Function and homology information


negative regulation of chemokine activity / lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / chemokine binding / astrocyte cell migration / regulation of behavior / CCR5 chemokine receptor binding ...negative regulation of chemokine activity / lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / chemokine binding / astrocyte cell migration / regulation of behavior / CCR5 chemokine receptor binding / eosinophil degranulation / CCR chemokine receptor binding / regulation of sensory perception of pain / signaling / negative regulation of bone mineralization / positive regulation of microglial cell activation / cell activation / T cell chemotaxis / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / response to cholesterol / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / phospholipase activator activity / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / exocytosis / cellular response to interleukin-1 / host-mediated suppression of viral transcription / neutrophil chemotaxis / cytoskeleton organization / positive regulation of calcium-mediated signaling / positive regulation of interleukin-1 beta production / cell chemotaxis / calcium-mediated signaling / cellular response to type II interferon / response to toxic substance / intracellular calcium ion homeostasis / chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / osteoblast differentiation / cellular response to tumor necrosis factor / calcium ion transport / kinase activity / cell-cell signaling / positive regulation of neuron apoptotic process / MAPK cascade / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #100 / Evasins Class A / Evasins Class A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily ...Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #100 / Evasins Class A / Evasins Class A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Evasin-1 / C-C motif chemokine 3
Similarity search - Component
Biological speciesRhipicephalus sanguineus (brown dog tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsShaw, J.P. / Dias, J.M.
Citation
Journal: Plos One / Year: 2009
Title: Structural basis of chemokine sequestration by a tick chemokine binding protein: the crystal structure of the complex between Evasin-1 and CCL3
Authors: Dias, J.M. / Losberger, C. / Deruaz, M. / Power, C.A. / Proudfoot, A.E.I. / Shaw, J.P.
#1: Journal: J.Biol.Chem. / Year: 2007
Title: Molecular cloning and characterization of a highly selective chemokine-binding protein from the tick Rhipicephalus sanguineus.
Authors: Frauenschuh, A. / Power, C.A. / Deruaz, M. / Ferreira, B.R. / Silva, J.S. / Teixeira, M.M. / Dias, J.M. / Martin, T. / Wells, T.N.C. / Proudfoot, A.E.I.
#2: Journal: J.Exp.Med. / Year: 2008
Title: Ticks produce highly selective chemokine binding proteins with antiinflammatory activity
Authors: Deruaz, M. / Frauenschuh, A. / Alessandri, A.L. / Dias, J.M. / Coelho, F.M. / Russo, R.C. / Ferreira, B.R. / Graham, G.J. / Shaw, J.P. / Wells, T.N.C. / Teixeira, M.M. / Power, C.A. / Proudfoot, A.E.I.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Evasin-1
B: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3084
Polymers19,1902
Non-polymers1172
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-11 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.384, 104.384, 104.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-101-

NI

21A-102-

NI

31B-71-

HOH

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Components

#1: Protein Evasin-1


Mass: 11306.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick)
Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P0C8E7
#2: Protein C-C motif chemokine 3 / Small-inducible cytokine A3 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / Tonsillar ...Small-inducible cytokine A3 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / Tonsillar lymphocyte LD78 alpha protein / G0/G1 switch regulatory protein 19-1 / G0S19-1 protein / SIS-beta / PAT 464.1 / MIP-1-alpha(4-69) / LD78-alpha(4-69)


Mass: 7883.808 Da / Num. of mol.: 1 / Mutation: A10T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10147
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 24% (w/v) PEG 3350, 200mM Ammonium sulfate, 100mM HEPES, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.976 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 17, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 19881 / Num. obs: 19881 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40.4 % / Rsym value: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 1.76→1.9 Å / Mean I/σ(I) obs: 7.8 / Rsym value: 0.828 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3fpr

3fpr


Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.868 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28467 1015 5.1 %RANDOM
Rwork0.23133 ---
all0.23398 18797 --
obs0.23398 18797 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.301 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 2 160 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211347
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.941832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48124.20369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.595159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021063
X-RAY DIFFRACTIONr_nbd_refined0.210.2570
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.219
X-RAY DIFFRACTIONr_mcbond_it1.3181.5845
X-RAY DIFFRACTIONr_mcangle_it2.27521341
X-RAY DIFFRACTIONr_scbond_it2.9813565
X-RAY DIFFRACTIONr_scangle_it4.294.5491
LS refinement shellResolution: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 75 -
Rwork0.265 1371 -
obs--100 %

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