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- PDB-8fj2: Crystal Structure of the Tick Evasin EVA-AAM1001(C8) Complexed to... -

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Basic information

Entry
Database: PDB / ID: 8fj2
TitleCrystal Structure of the Tick Evasin EVA-AAM1001(C8) Complexed to Human Chemokine CCL17
Components
  • C-C motif chemokine 17
  • Evasin P1243
KeywordsCYTOKINE / Evasin / Chemokine-binding protein / ticks
Function / homology
Function and homology information


negative regulation of chemokine activity / chemokine binding / C-C chemokine binding / chemokine activity / Chemokine receptors bind chemokines / chemotaxis / cell-cell signaling / immune response / inflammatory response / signaling receptor binding ...negative regulation of chemokine activity / chemokine binding / C-C chemokine binding / chemokine activity / Chemokine receptors bind chemokines / chemotaxis / cell-cell signaling / immune response / inflammatory response / 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: 2.07 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 19, 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 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,3672
Polymers19,3672
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.641, 62.536, 92.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

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Components

#1: Protein Evasin P1243


Mass: 11270.512 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.: 43 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4.3 M NaCl, 0.1 M HEPES pH 7.4

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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: Aug 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.07→46.34 Å / Num. obs: 10995 / % possible obs: 99.3 % / Redundancy: 12.7 % / Biso Wilson estimate: 33.58 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.7
Reflection shellResolution: 2.07→2.13 Å / Num. unique obs: 785 / CC1/2: 0.551

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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 / Resolution: 2.07→43.53 Å / SU ML: 0.2469 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 510 4.66 %
Rwork0.213 10424 -
obs0.214 10934 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.2 Å2
Refinement stepCycle: LAST / Resolution: 2.07→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 0 43 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121073
X-RAY DIFFRACTIONf_angle_d1.21071460
X-RAY DIFFRACTIONf_chiral_restr0.0945171
X-RAY DIFFRACTIONf_plane_restr0.0126187
X-RAY DIFFRACTIONf_dihedral_angle_d15.5983153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.280.33651230.2842520X-RAY DIFFRACTION97.93
2.28-2.610.29641040.24982597X-RAY DIFFRACTION99.82
2.61-3.290.30781080.23062642X-RAY DIFFRACTION100
3.29-43.530.18981750.18172665X-RAY DIFFRACTION99.27
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)
18.47447881776-0.9100662068050.33170282284.635287339134.88149247035.329718643140.009295035072440.761968670253-0.125014277604-0.5408290854560.03470126087860.106107260398-0.601435424595-0.285411226335-0.1885592484030.427528220834-0.003905201817510.07804250320140.417187987628-0.03260694744680.388637171406-14.1261297847-11.7910388432-16.8157822516
27.83258475102-1.55003848541-0.08545255271843.4789247280.616873159377.749074549760.0405187514095-0.0179932813018-0.5077851929640.1856685962940.115904518663-0.05377688260060.692058189528-0.052312757817-0.2360881829820.410185507443-0.0167834837066-0.009370429915660.29140455871-0.02732014215450.375171659983-16.2953365123-14.7261770304-11.2487092755
35.903164382821.53600999855-5.164850207882.64474527543-0.9275993184455.069196631970.5384113070621.073698186080.654165983980.815288053855-0.6396188607520.408120847439-0.800309200507-2.320553856620.1732875898810.45428820660.08006465222080.08800884581430.6501569253010.001757385347460.44478054142-28.3305890727-4.51758605642-6.49690386744
44.89957940623-1.89693553475-1.662696702694.88432235161.080393999933.03808713805-0.188870674545-0.418939547710.2598570779420.01036198143290.20480247438-0.2899064348010.02767900387670.318556192397-0.05208146417910.4891228664380.01895224783-0.02812058891250.460881649541-0.07193473007230.392865097896-17.4140725551-7.69936643117-5.26808595238
56.50598114114-1.51215988337-2.8844938473.609786198642.483903991992.31935509141-0.461066581490.581755753171-0.373078063495-0.7573244717990.480939733413-0.2302789431320.05554155754410.448020557556-0.1013254376880.589931635173-0.01136506036420.04503387870140.529793707817-0.1152975314310.439025987112-8.00573161786-18.6825530195-23.1204277779
66.23022021493-0.897169944631-5.228095156362.558183025131.76359658954.926497072460.1989057471940.2727597460170.3275268561690.000348664276242-0.11273555996-0.113370091104-0.177638621052-0.3341806567510.03990907764590.4196028139120.107990216702-0.004958063236470.424522489752-0.07007790932590.417752806543-2.53463571001-15.9098363939-28.1204863929
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 33 )AA23 - 331 - 11
22chain 'A' and (resid 34 through 65 )AA34 - 6512 - 43
33chain 'A' and (resid 66 through 71 )AA66 - 7144 - 49
44chain 'A' and (resid 72 through 103 )AA72 - 10350 - 81
55chain 'B' and (resid 8 through 20 )BB8 - 201 - 13
66chain 'B' and (resid 21 through 68 )BB21 - 6814 - 61

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