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- PDB-8fj3: Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Hum... -

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Basic information

Entry
Database: PDB / ID: 8fj3
TitleCrystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL7(Y13A)
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: 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 7


Theoretical massNumber of molelcules
Total (without water)19,9972
Polymers19,9972
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.272, 72.272, 65.535
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

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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 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: 8882.387 Da / Num. of mol.: 1 / Mutation: Y13A
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.: 78 / 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: 42.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2 M NH2SO4, 0.1 Na acetate, pH 4.8

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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: Jul 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→48.55 Å / Num. obs: 11114 / % possible obs: 99.9 % / Redundancy: 24.5 % / Biso Wilson estimate: 28.7 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.1
Reflection shellResolution: 2.07→2.13 Å / Num. unique obs: 846 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→40.3 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 564 5.09 %
Rwork0.2135 10506 -
obs0.2143 11070 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.11 Å2
Refinement stepCycle: LAST / Resolution: 2.07→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 0 78 1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191104
X-RAY DIFFRACTIONf_angle_d1.67541504
X-RAY DIFFRACTIONf_chiral_restr0.0934177
X-RAY DIFFRACTIONf_plane_restr0.0077194
X-RAY DIFFRACTIONf_dihedral_angle_d3.9878156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.280.25841410.22662540X-RAY DIFFRACTION99.48
2.28-2.610.25671510.22832573X-RAY DIFFRACTION100
2.61-3.280.23061300.2222634X-RAY DIFFRACTION99.96
3.28-40.30.21191420.2022759X-RAY DIFFRACTION99.93
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)
12.898787735573.41100912318-2.760529987984.67007524931-1.655581529655.18205565181-0.2222705087860.642323701255-0.109093832787-0.03126043939810.311203531067-0.07709362176890.337707389321-0.168135807252-0.114000201840.2156314336450.0349293841524-0.01437112921690.17032951859-0.02068278777630.174105468846-27.426887794-10.3973478606-3.49880996709
25.57304122031-1.390927185252.442025933680.470403191987-0.05344018061014.04172216372-0.00883985060277-0.223418129716-0.244387097546-0.4368128938790.4793686387050.4598072637270.561192464657-0.644624820134-0.4477770731240.318235140862-0.070199841209-0.1171002763260.3113522040460.07101422224450.214768391324-36.566999931-6.62573204084-6.24328942785
31.71396158785-0.0188942277067-0.781332912662.64553301115-0.9860576377093.583427003910.01012537468090.1433807511180.02025122227580.0514929159010.2809127110210.2321306230430.105001995477-0.630669657394-0.2164651072390.216901044396-0.0212417449065-0.0269295562990.2661884616940.02112544007950.199986829377-33.6774657251-4.26712360059-3.17497138046
45.93429001958-1.677938448332.238635564534.25737298915-1.207053619323.544849856240.00883021148920.4841676078530.519440811636-0.0873021539185-0.291126760747-0.305546023027-0.2973929584320.6629521565650.275216921150.249844324413-0.01532254812210.04496516174120.3822428568280.01489660302410.281467641688-21.2783520084-2.42906278606-15.5766494449
59.9476529688-3.73108764122-4.622025789646.19170063781.585981750674.881472261310.172831767444-0.6832188049710.2309933320950.2536425781360.253527474553-0.02653857931220.424924765494-0.226226957011-0.3953361292250.334394798563-0.0416574913423-0.0537276194530.28080997637-0.01180309611890.187529111633-28.6872468721.46550036060.415558543079
65.88759361295-1.79082389506-2.136803793483.060042625371.058793641332.997311272240.123695627680.308113207342-0.1915171820110.0306160221748-0.0757387903419-0.3722418567090.007722486131410.172603633375-0.01724812982430.181237945723-0.0216361035253-0.03374674404270.186216381646-0.01126118516960.21633673384-23.9675213716-1.43562047074-5.05660788837
71.614156496351.72476669871.609434782315.60280489576-0.2007617308622.387264643140.06605882760550.05405919799-0.3291648193830.355856666193-0.0806595300888-0.006381740648840.363975567108-0.2941268878160.04488216898940.316762335682-0.0291374475424-0.05532973906820.2999192711420.001463281783640.255299864124-35.8398982802-16.65230058732.40366522145
82.773575139254.21604910087-1.032890541016.52017359151-0.9963056120626.36535193431-0.411557912849-0.279732566712-0.765263034747-0.39252974227-0.0204353489138-0.1117059496260.6810427510620.09240162793720.3037309989480.334517680407-0.00180204058375-0.02937619759270.3524428719330.0293676548910.729772172306-39.4922642282-28.17707191840.610617341655
98.065466111744.70638625999-0.2306703006844.50576913355-1.020437302711.480716805820.0890266525683-0.0841977036508-0.770434571826-0.28273788666-0.00794265168487-0.3088557382510.0603824627762-0.0240308158784-0.0832458031280.2363297864450.000452021810374-0.06016698398860.1943745955130.01267279522820.268670093467-34.504142176-20.22204007070.367732403963
106.876937462372.924086803563.138673201618.41574752744-1.6504281326.335511794250.74602612575-1.73496969341-0.06144236212251.57506434309-0.932248297344-0.647335855963-0.4743063755990.7658571186930.1325055926970.4225232458-0.0983527962937-0.1434406525360.4737529942270.163862967730.409552520603-35.9155330049-19.74737150726.11389330909
118.01735662841.692410548660.6243887453964.60609617815-1.872548850978.001981447570.50461618449-1.27018641481-1.701701710881.43565997528-1.07548171917-2.169046187770.4615018908791.06148689530.2937492233690.536913633693-0.10460332333-0.1212869107950.6873494310350.3437439218330.868615499988-36.1186283287-30.65859396128.63506040509
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 41 )AA22 - 411 - 20
22chain 'A' and (resid 42 through 48 )AA42 - 4821 - 27
33chain 'A' and (resid 49 through 65 )AA49 - 6528 - 44
44chain 'A' and (resid 66 through 80 )AA66 - 8045 - 59
55chain 'A' and (resid 81 through 86 )AA81 - 8660 - 65
66chain 'A' and (resid 87 through 103 )AA87 - 10366 - 82
77chain 'B' and (resid 7 through 21 )BB7 - 211 - 15
88chain 'B' and (resid 22 through 31 )BB22 - 3116 - 25
99chain 'B' and (resid 32 through 49 )BB32 - 4926 - 43
1010chain 'B' and (resid 50 through 57 )BB50 - 5744 - 51
1111chain 'B' and (resid 58 through 70 )BB58 - 7052 - 64

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