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- PDB-7scs: Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Hum... -

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Basic information

Entry
Database: PDB / ID: 7scs
TitleCrystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL11
Components
  • Eotaxin
  • Evasin P1243
KeywordsIMMUNE SYSTEM / Chemokine / Evasin / Ticks / Inflammation
Function / homology
Function and homology information


response to interleukin-13 / CCR3 chemokine receptor binding / negative regulation of chemokine activity / chronic inflammatory response / response to interleukin-4 / chemokine binding / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis ...response to interleukin-13 / CCR3 chemokine receptor binding / negative regulation of chemokine activity / chronic inflammatory response / response to interleukin-4 / chemokine binding / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / branching involved in mammary gland duct morphogenesis / chemokine activity / positive regulation of actin filament polymerization / monocyte chemotaxis / cellular response to interleukin-1 / positive regulation of endothelial cell proliferation / cytoskeleton organization / ERK1 and ERK2 cascade / neutrophil chemotaxis / actin filament organization / response to virus / response to radiation / positive regulation of GTPase activity / negative regulation of neurogenesis / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of angiogenesis / chemotaxis / cellular response to tumor necrosis factor / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor ligand activity / learning or memory / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / cell adhesion / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signal transduction / extracellular space / extracellular region
Similarity search - Function
Evasins Class A / Evasins Class A / 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
Similarity search - Domain/homology
Evasin P1243 / Eotaxin
Similarity search - Component
Biological speciesAmblyomma americanum (Lone Star tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsDevkota, S.R. / Bhusal, R.P. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Citation
Journal: Nat Commun / Year: 2023
Title: Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins.
Authors: Devkota, S.R. / Aryal, P. / Pokhrel, R. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R.J. / Wilce, M.C.J. / Bhusal, R.P. / Stone, M.J.
#1: Journal: Res Sq / Year: 2023
Title: Engineering Broad-spectrum Inhibitors of Inflammatory Chemokines from a New Family of Tick Evasins
Authors: Devkota, S. / Aryal, P. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R. / Wilce, M. / Bhusal, R. / Stone, M.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Evasin P1243
B: Eotaxin


Theoretical massNumber of molelcules
Total (without water)19,4952
Polymers19,4952
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.028, 75.028, 66.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Evasin P1243


Mass: 11114.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amblyomma americanum (Lone Star tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C9S461
#2: Protein Eotaxin / / C-C motif chemokine 11 / Eosinophil chemotactic protein / Small-inducible cytokine A11


Mass: 8380.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL11, SCYA11 / Production host: Escherichia coli (E. coli) / References: UniProt: P51671
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS 6.5 pH (Buffer) , 2 M (NH4)2SO4 (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.51→41.58 Å / Num. obs: 56735 / % possible obs: 99.8 % / Redundancy: 25.6 % / Biso Wilson estimate: 21.22 Å2 / CC1/2: 1 / Net I/σ(I): 23.9
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 1433 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S58

7s58


Resolution: 1.51→41.58 Å / SU ML: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2065 2977 5.25 %
Rwork0.1844 53758 -
obs0.1856 56735 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.59 Å2
Refinement stepCycle: LAST / Resolution: 1.51→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 0 157 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091198
X-RAY DIFFRACTIONf_angle_d1.20981623
X-RAY DIFFRACTIONf_chiral_restr0.0605185
X-RAY DIFFRACTIONf_plane_restr0.0069206
X-RAY DIFFRACTIONf_dihedral_angle_d14.8497168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.35551210.27182451X-RAY DIFFRACTION95.44
1.54-1.570.24241470.2372606X-RAY DIFFRACTION99.96
1.57-1.590.27981380.23042556X-RAY DIFFRACTION100
1.59-1.620.22471470.22582532X-RAY DIFFRACTION100
1.62-1.660.25391140.20942603X-RAY DIFFRACTION100
1.66-1.690.23541540.2152550X-RAY DIFFRACTION99.96
1.69-1.730.22761490.20882574X-RAY DIFFRACTION100
1.73-1.780.25091320.19672553X-RAY DIFFRACTION99.93
1.78-1.820.22581530.18552581X-RAY DIFFRACTION100
1.82-1.880.21721310.1892561X-RAY DIFFRACTION99.96
1.88-1.940.21511310.18842570X-RAY DIFFRACTION100
1.94-2.010.24731570.17722562X-RAY DIFFRACTION100
2.01-2.090.20471640.18012543X-RAY DIFFRACTION100
2.09-2.180.19531610.18532550X-RAY DIFFRACTION100
2.18-2.30.21331470.17812555X-RAY DIFFRACTION100
2.3-2.440.20741480.18752576X-RAY DIFFRACTION100
2.44-2.630.23331420.20292545X-RAY DIFFRACTION100
2.63-2.90.17731220.1972607X-RAY DIFFRACTION99.96
2.9-3.310.19461190.1792571X-RAY DIFFRACTION99.93
3.31-4.170.19491510.15992570X-RAY DIFFRACTION99.96
4.18-41.580.18761490.1762542X-RAY DIFFRACTION99.23
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)
15.645925252262.966958593212.193017129683.375666831951.432860560292.478504813650.0295991982710.260845494782-0.314403633440.04255499246930.143324203541-0.345307475238-0.4625571330720.714491570450.004028721074480.440073191497-0.0942317541050.05549387204410.3007874459180.006434650342120.231625879745-16.274368229817.7810255463-3.5944124529
27.1846347239-2.24143086310.4085134858752.88355568134-0.07252667147974.83933896362-0.223134805994-0.126898896789-0.2790906619650.1058673873180.09565193785580.1880547233840.0731168565478-0.2920383534180.1478742010830.141688849314-0.01165955273830.003109629814740.0995377967846-0.002835033487290.163210763933-31.03676449926.10634379869-13.6358427697
35.55648070840.2144828604640.4708931487972.044452489950.4027164224012.682657366380.0523644022809-0.4554901542230.1690465901460.6514776993230.008764221878980.0980445301562-0.193164317082-0.0307430749632-0.03709794656750.283831698392-0.06010614752440.06575306252160.192211070317-0.002715718646340.228829730318-15.606865212716.1664738672-11.3931399735
41.908675427420.7831509720860.2264051845832.19145608788-0.8354709265454.704847104460.0171465605990.0680605099866-0.0874776174997-0.0613930084771-0.0952123490377-0.1055306670690.07179043662730.1146025452390.06861563384530.1530816045960.0009073413425590.008153415714890.13377255050.02219263346720.167143937535-22.77500818434.38039557724-14.5927401973
53.42775404593-0.569488902024-0.6940514232940.472350601704-0.08230705566612.37564355144-0.04350614964170.237641444415-0.098010939549-0.12152986094-0.1019296979-0.07428925612690.0228080478181-0.07259890805650.1251904563950.1986874340430.0132074857798-0.03800737547790.2286221007520.01366516263540.24245705143-31.423080882610.9138050188-25.9521998725
65.834266288640.3030790499471.884581048163.347880076680.8748219597152.412782492160.06002679346060.195138886-0.236488094111-0.111940425815-0.0557065560936-0.08956869075960.06389791967070.12857221793-0.01646041496310.2174654072650.001899104503380.02502939968620.1494264606270.003150461583460.203533380658-24.1320646957-0.121934205206-17.3015893616
72.189270862890.648330331434-0.621508144062.59225769954.012159632067.7229094921-0.23921707175-0.009836145640260.3481851988650.04230560514030.402124225084-0.243205971708-0.4699814192070.134962083831-0.1148475061260.2413553231720.0355927276146-0.05548923922880.210515726964-0.02520701713570.259508509018-33.853574408212.9690849075-16.7284521452
83.801991271873.429772357551.107946173563.3560149676-0.3663208075888.7075916933-0.1327248266460.2504541925680.8373735542560.0921200192948-0.129351654820.150162527712-0.579910889925-0.8495328549710.1829795768330.5017614060710.079848844301-0.04982766615570.393707615647-0.006048847892790.390202005891-34.460342668314.83071784-7.05940326112
90.799644627236-0.7243060780230.1551020458032.697646747451.235182611.11482186813-0.113800127252-0.11446348938-0.1312384513730.1524700664080.206642960227-0.0589363256985-0.371945138219-0.03592663790280.06418605111820.449999902364-0.01917708782020.05317418052210.232344406308-0.01465276985040.33970595614-22.309650543911.5658065101-3.40250537642
106.910294880540.73656099939-0.765823047296.402818185170.6688792089794.32593151856-0.0484351187917-0.198003197049-0.03638370517270.00756249493013-0.1037779247670.02388464425720.04644567900240.05124502495880.1332518680810.248177787622-0.04747056890170.01714028714210.2062456778610.01652502991620.154506651333-22.536209619121.03829790486.13809298887
112.696463913663.061327918691.772365463586.701359761224.612633056544.420554358010.381920685157-0.2127036671960.2252667217470.294040435776-0.7530024026160.5134764176970.376641502606-0.3103597861530.3321329006640.259843410967-0.03414168442580.005912868695710.182816403685-0.005224090318470.198527652236-28.594514254313.8349394253-0.326511489322
123.947722048180.859072387983-0.78966267541.5392030566-2.097599945986.31838678663-0.269906159538-0.0694870190046-0.104532843985-0.4309668780870.4471693618070.2510073427630.616449722194-0.133832479519-0.1985167253580.329658658974-0.02650003004390.02747677512270.230873513598-0.003044956864460.217090966019-22.302468147419.07044856122.88512973504
138.38368423892-2.564438391410.4463260701682.05982977566-0.7445890903276.20620359163-0.024160031115-0.2425332594030.2366276275280.486007190616-0.1587429464860.4035586022830.0824310012964-0.4957356129540.2038890391630.270598364123-0.0757319213660.02712670907870.270115297418-0.04526431111290.185979968665-26.273616929821.270790918712.9139733646
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 28 )AA15 - 281 - 14
22chain 'A' and (resid 29 through 42 )AA29 - 4215 - 28
33chain 'A' and (resid 43 through 52 )AA43 - 5229 - 38
44chain 'A' and (resid 53 through 63 )AA53 - 6339 - 49
55chain 'A' and (resid 64 through 78 )AA64 - 7850 - 65
66chain 'A' and (resid 79 through 96 )AA79 - 9666 - 83
77chain 'A' and (resid 97 through 101 )AA97 - 10184 - 88
88chain 'B' and (resid 4 through 8 )BB4 - 81 - 5
99chain 'B' and (resid 9 through 13 )BB9 - 136 - 10
1010chain 'B' and (resid 14 through 29 )BB14 - 2911 - 26
1111chain 'B' and (resid 30 through 43 )BB30 - 4327 - 40
1212chain 'B' and (resid 44 through 55 )BB44 - 5541 - 52
1313chain 'B' and (resid 56 through 68 )BB56 - 6853 - 65

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