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

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Basic information

Entry
Database: PDB / ID: 7scv
TitleCrystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL17
Components
  • C-C motif chemokine 17
  • Evasin P1243
KeywordsIMMUNE SYSTEM / Inflammation / Chemokine / Ticks / Evasin
Function / homology
Function and homology information


negative regulation of chemokine activity / chemokine binding / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 ...negative regulation of chemokine activity / chemokine binding / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / cellular response to type II interferon / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / 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 / C-C motif chemokine 17
Similarity search - Component
Biological speciesAmblyomma americanum (Lone Star tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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

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Assembly

Deposited unit
A: Evasin P1243
B: C-C motif chemokine 17


Theoretical massNumber of molelcules
Total (without water)19,2112
Polymers19,2112
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-15 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.900, 87.900, 54.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-259-

HOH

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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 C-C motif chemokine 17 / CC chemokine TARC / Small-inducible cytokine A17 / Thymus and activation-regulated chemokine


Mass: 8096.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL17, SCYA17, TARC / Production host: Escherichia coli (E. coli) / References: UniProt: Q92583
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Acet 4.6 pH (Buffer),2 M NaCl (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: 2.01→44.56 Å / Num. obs: 16587 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 1 / Net I/σ(I): 24.7
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 1196 / CC1/2: 0.869

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Processing

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

7scs


Resolution: 2.01→44.56 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.3704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 914 5.51 %
Rwork0.2367 15662 -
obs0.2375 16576 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.41 Å2
Refinement stepCycle: LAST / Resolution: 2.01→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 0 88 1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241109
X-RAY DIFFRACTIONf_angle_d0.60651501
X-RAY DIFFRACTIONf_chiral_restr0.0395171
X-RAY DIFFRACTIONf_plane_restr0.0026191
X-RAY DIFFRACTIONf_dihedral_angle_d4.6486159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.120.2981440.26892205X-RAY DIFFRACTION99.91
2.12-2.250.29451200.25152208X-RAY DIFFRACTION99.91
2.25-2.420.25471380.26632189X-RAY DIFFRACTION100
2.43-2.670.30381220.27862238X-RAY DIFFRACTION100
2.67-3.050.28791170.26782248X-RAY DIFFRACTION100
3.05-3.850.22771270.22342247X-RAY DIFFRACTION100
3.85-44.560.23511460.21482327X-RAY DIFFRACTION99.96
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)
12.460626032591.16052131785-1.756460324.326850207163.37918658216.206664077220.268187155844-0.238207041725-0.040445430069-1.98400809993-0.1753394258730.6491072480810.38391059164-1.30340472477-0.1713669798310.735766785152-0.185308897986-0.1266906284640.4799649732630.04586612168080.504591611215-11.674884390956.597122576621.1916779027
25.758040489140.0676042726267-1.221060676195.817789125630.1279952742828.819686626530.19212736699-0.367584045118-0.6909683413610.759286906839-0.213208379702-0.7952546515461.522542533080.9662486401530.03386252303660.582405872761-0.00529942191511-0.09615425359950.307232774010.03389040595290.498812263786.8575016903358.103459203232.8158739327
34.285368709780.7112536181650.360302552824.47113710684-2.120687155695.66450745541-0.2287692678870.5095197547940.0637888565607-0.250947160350.154966267978-0.195067771584-0.2371708756320.2313212298190.161438341130.439533168283-0.05496313200740.03281674631460.2597653601780.01713365509830.255368642061-0.90115091955863.406232691425.0857701232
44.38902061080.927279989547-0.5758325581485.46117975572-0.6029274414544.99351520863-0.1778683649650.03682568124520.114481488373-0.210215759228-0.0601616782881-0.2236531746670.2399959262110.1791823617230.2077750938250.452992945806-0.02765279627510.03444240828930.2534690615170.02575027175750.3674909418332.394382099466.843270506525.462156344
53.88502137874-5.009551720234.053410351587.12384471846-5.338243341464.75572439387-0.886840713384-1.023610539611.247701995740.09950574765550.0806602261343-3.54267511233-0.2085047859750.6806488891790.5852974063820.4468512552630.0650334357641-0.0854002166810.6880697700040.001313011742980.82185406742116.802922614860.254457512927.0939806999
65.23227313877-0.0548534236021-0.08879691470654.846553938220.8010888693232.97132618821-0.145155148503-0.0634559513157-0.1177417011560.773896687335-0.0411648495794-0.1476245158560.06760602841230.1665627085970.2314572019670.584581741677-0.0674904225444-0.04097925946890.3165006956260.00681396679410.3929211853344.3932527236370.430902327433.684393606
72.12708466791.926766873172.393387710121.787963490631.576602831159.739896820250.30211228110.1381435118430.1102407568410.79688158397-0.444735476092-1.689952392171.160691007950.2867853048290.2666811500590.4882853900840.0973514395084-0.1004170805090.4427297491480.07609526037810.56335893201411.740379850757.344356860127.3785189723
85.827065021953.576935563182.082315375914.198674897840.7243773659262.946905896020.4926146564280.351623561363-0.134465525903-0.116703407379-0.2155134221450.4864400470630.117526604142-0.139733113533-0.1887914748910.4840446720120.01160910124040.01616828947760.339236994173-0.02045132925490.377477948967-10.243199288353.868363499727.0207096073
94.615862647074.000986860642.790423736625.195294693892.102105869263.657254330510.08034339066790.0326070919996-0.5449216827170.07842584968710.237925422266-0.477432325840.01763200754150.0145420810274-0.2616586015890.388127781515-0.07683821933640.0337104561190.3669415551980.00150660624180.408431332207-8.3528571593347.323438353727.3278192218
105.259163014111.719245419111.714641013237.216597414660.8086730557435.734779762410.0715943743503-0.0265706477142-0.431710262828-0.02911042378130.128162692410.5834272977710.0128108040147-0.243722951719-0.1892905527680.303107703838-0.106838339598-0.02085762282630.45415333069-0.004594944540170.441602445413-14.041520526943.444296899527.5271208317
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 26 )AA17 - 261 - 10
22chain 'A' and (resid 27 through 36 )AA27 - 3611 - 20
33chain 'A' and (resid 37 through 46 )AA37 - 4621 - 30
44chain 'A' and (resid 47 through 69 )AA47 - 6931 - 53
55chain 'A' and (resid 70 through 76 )AA70 - 7654 - 60
66chain 'A' and (resid 77 through 96 )AA77 - 9661 - 80
77chain 'A' and (resid 97 through 101 )AA97 - 10181 - 85
88chain 'B' and (resid 7 through 20 )BB7 - 201 - 14
99chain 'B' and (resid 21 through 43 )BB21 - 4315 - 37
1010chain 'B' and (resid 44 through 69 )BB44 - 6938 - 63

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