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- PDB-8fk8: Crystal Structure of the Tick Evasin EVA-AAM1001(L39P) Complexed ... -

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Basic information

Entry
Database: PDB / ID: 8fk8
TitleCrystal Structure of the Tick Evasin EVA-AAM1001(L39P) Complexed to Human Chemokine CCL7
Components
  • C-C motif chemokine 7
  • Evasin P1243
KeywordsCYTOKINE / Evasin / Chemokine-binding protein / ticks
Function / homology
Function and homology information


negative regulation of chemokine activity / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / chemokine binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / chemokine activity ...negative regulation of chemokine activity / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / chemokine binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / chemokine activity / Chemokine receptors bind chemokines / monocyte chemotaxis / cellular response to ethanol / cytoskeleton organization / response to gamma radiation / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / regulation of cell shape / heparin binding / positive regulation of cell migration / inflammatory response / 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 / C-C motif chemokine 7
Similarity search - Component
Biological speciesAmblyomma americanum (Lone Star tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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)APP1140867 Australia
CitationJournal: 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.
History
DepositionDec 20, 2022Deposition 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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 P1243
B: C-C motif chemokine 7


Theoretical massNumber of molelcules
Total (without water)20,2612
Polymers20,2612
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-15 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.502, 72.502, 65.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-115-

HOH

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Components

#1: Protein Evasin P1243


Mass: 11286.600 Da / Num. of mol.: 1 / Mutation: L39P
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 7 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small- ...Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7


Mass: 8974.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL7, MCP3, SCYA6, SCYA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80098
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium sulfate

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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 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.96→48.78 Å / Num. obs: 23718 / % possible obs: 100 % / Redundancy: 25.5 % / Biso Wilson estimate: 31.63 Å2 / CC1/2: 0.99 / Net I/σ(I): 18.2
Reflection shellResolution: 1.96→2.01 Å / Num. unique obs: 903 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→48.78 Å / SU ML: 0.2015 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 1195 5.04 %
Rwork0.2412 22523 -
obs0.2424 23718 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.46 Å2
Refinement stepCycle: LAST / Resolution: 1.96→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 52 1078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01881047
X-RAY DIFFRACTIONf_angle_d1.79661427
X-RAY DIFFRACTIONf_chiral_restr0.0992168
X-RAY DIFFRACTIONf_plane_restr0.007183
X-RAY DIFFRACTIONf_dihedral_angle_d3.9142150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.040.27471340.27352510X-RAY DIFFRACTION99.36
2.04-2.130.31351240.26892585X-RAY DIFFRACTION100
2.13-2.250.34411360.32332371X-RAY DIFFRACTION94.85
2.25-2.390.33621290.30492380X-RAY DIFFRACTION94.08
2.39-2.570.2771310.26242545X-RAY DIFFRACTION99.96
2.57-2.830.26351270.26142530X-RAY DIFFRACTION100
2.83-3.240.27041270.2342547X-RAY DIFFRACTION100
3.24-4.080.24851580.2082522X-RAY DIFFRACTION99.78
4.08-48.780.22711290.22142533X-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)
15.085651861582.843584397591.779287559882.98474725991.456402249652.086189537820.1191227029281.125174799830.2177326732731.751500739271.143369090093.31831493547-0.123559669624-1.94278665354-1.300189463950.4401445848550.01316938566660.099880895660.567406168270.1742073985010.653388113452-43.252-12.3190.931
26.060456459575.52952843775-5.985077466885.08719839123-5.464037524425.91422176765-0.445042571121.83165381188-0.0011866198588-0.3558866460630.4566502095980.6534521038820.256699466736-0.5117310716020.04601193329360.343848110468-0.0132826793771-0.07110581443740.352591735782-0.03343325952370.301227497893-32.458-13.376-5.818
36.602677348835.16885475911-6.348143638446.71342534066-2.626291112048.88534575736-0.2039309747-0.261109520862-0.5401257269620.00818218861807-0.124971383066-0.7301844830660.357622174970.7692090897590.3183585911870.2154337447590.0451380467844-0.0621939871210.276622497508-0.03258987627050.360718547694-19.779-8.685-3.567
42.38487909156-0.0371783837130.23823286333.562579156493.157811550712.876749638320.454575863356-0.369911255903-0.309267016396-0.6859448668650.2001757448870.2936136262280.47353924621-1.07373117258-0.2195182276670.3434605811-0.117733987483-0.1581010830520.4544950524490.146598737490.236626074959-36.093-6.306-5.963
51.29426346432-0.526068797449-1.390573466793.96554374387-1.202358415982.40886806228-0.1618579129540.4634229742150.330455251616-0.1707708453310.5169432838030.3911322040190.0885480348447-0.868992322761-0.2062427230220.276983721148-0.062408306592-0.03173616261660.3644689154440.02429836788270.225772685509-33.497-3.552-3.049
65.193885250070.412123645381-2.637247005042.756728712633.834948130998.21816913332-0.0199299340750.3516323622870.348785037628-1.26184502164-0.223091719399-0.678341281668-0.8043815315870.3138384777740.1874603787040.430646211093-0.0193422532920.05410367264390.3635919341330.06103692509490.452914203945-25.9261.536-17.287
78.39553291-2.67689428122-3.553688080615.76764635941.537868826434.00815828150.1628326601220.4014428789550.314855357988-0.158973825359-0.104211923805-0.496222642144-0.223657221870.160525819493-0.1041942399230.219977056765-0.024513488642-0.03617477652660.2613153623250.008040278127390.23555264608-24.936-0.656-7.394
83.76385002236-2.6629805403-1.213965180619.375046770814.687558614922.375715803970.07823490827140.09043823342950.060540901290.499619709250.215993223544-0.7220269551250.08632590189620.550043908033-0.1520699289930.314386601153-0.0399142883740.002882434556270.2941057249390.002506754007650.463988524141-19.531-3.395-6.185
94.873897134423.38105000523.155055605918.769184161160.340643939722.678571118930.336847563186-0.308125217947-0.01186724346550.750382024551-0.2271428868460.480047155614-0.0240804429185-0.450085038678-0.05411015286870.268772563125-0.0436426228403-0.01414679690220.2771365603510.002230815246970.248975674642-36.642-16.3712.764
109.399098913115.857563446142.134792837986.917137423860.7997723747322.826762941240.321347314454-0.584570226703-1.16520667390.157800966322-0.111010401235-0.3078437881630.00655078245557-0.48901166816-0.1672372866490.389655459825-0.022206008027-0.09286693607020.4908883339210.03728291782640.957328771842-40.739-28.1091.414
116.303295842674.97024250815-2.898879853865.82039338962-2.310250450751.298145527610.54996690279-0.78416177285-0.8421356838740.404562393219-0.473248088234-0.3562931159940.219361274830.12549016053-0.0484097547880.334783681337-0.0450375251659-0.09616897602990.2828458121730.06222615195020.310129386785-34.63-19.7132.298
120.231018904150.465823859889-0.6157359977210.901022228167-1.206363082881.61444483399-0.076572074836-0.324580501726-0.476346934260.073114600742-0.27070275097-0.5224464339960.003993369169910.3825765868140.09575549482390.684593821172-0.504822727017-0.3731784824970.532248508030.8421181856540.892177610175-36.846-28.5949.469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 21:25 )A21 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:30 )A26 - 30
3X-RAY DIFFRACTION3( CHAIN A AND RESID 31:40 )A31 - 40
4X-RAY DIFFRACTION4( CHAIN A AND RESID 41:48 )A41 - 48
5X-RAY DIFFRACTION5( CHAIN A AND RESID 49:65 )A49 - 65
6X-RAY DIFFRACTION6( CHAIN A AND RESID 66:70 )A66 - 70
7X-RAY DIFFRACTION7( CHAIN A AND RESID 71:92 )A71 - 92
8X-RAY DIFFRACTION8( CHAIN A AND RESID 93:102 )A93 - 102
9X-RAY DIFFRACTION9( CHAIN B AND RESID 8:21 )B8 - 21
10X-RAY DIFFRACTION10( CHAIN B AND RESID 22:31 )B22 - 31
11X-RAY DIFFRACTION11( CHAIN B AND RESID 32:57 )B32 - 57
12X-RAY DIFFRACTION12( CHAIN B AND RESID 58:67 )B58 - 67

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