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- PDB-8fk6: Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed ... -

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Basic information

Entry
Database: PDB / ID: 8fk6
TitleCrystal Structure of the Tick Evasin EVA-AAM1001(Y44A) 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: 1.74 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
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
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Nov 6, 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)20,1852
Polymers20,1852
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-14 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.301, 72.301, 67.275
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: 11210.546 Da / Num. of mol.: 1 / Mutation: Y44A
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.: 103 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
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: Aug 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.74→49.25 Å / Num. obs: 18937 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 25.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 39.4
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 1025 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→40.7 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.6405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 906 4.8 %
Rwork0.2062 17977 -
obs0.207 18883 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.89 Å2
Refinement stepCycle: LAST / Resolution: 1.74→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 0 103 1226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361146
X-RAY DIFFRACTIONf_angle_d0.63211560
X-RAY DIFFRACTIONf_chiral_restr0.0454185
X-RAY DIFFRACTIONf_plane_restr0.004199
X-RAY DIFFRACTIONf_dihedral_angle_d10.7944405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.850.24991480.2082929X-RAY DIFFRACTION99.77
1.85-1.990.25961430.21152939X-RAY DIFFRACTION100
1.99-2.190.21221330.20332991X-RAY DIFFRACTION99.97
2.19-2.510.25711860.20762925X-RAY DIFFRACTION100
2.51-3.160.22481380.22133020X-RAY DIFFRACTION99.97
3.16-40.70.20531580.19833173X-RAY DIFFRACTION99.76
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)
18.94592602885-4.172221083964.072641722792.66502341520.2496233843698.28189750306-0.0929204050989-0.332237163472-0.4434529006890.878728331654-0.05660861695462.2596437931-0.353853724266-1.67394373520.17976637990.333015775203-0.01182632853070.1190519362930.4928394260130.01653724487260.470052581313-42.5964856467-12.0900639769-0.228611716054
22.409445575670.671868026625-0.7530140668873.22901673015-0.8588313935193.092222078620.0152651661576-0.0210332564782-0.1534019325210.1342331868180.0580239692474-0.1893009193490.0114264910757-0.0924156856381-0.06658428779460.167242428939-0.00376850816641-0.0353773874310.168951467577-0.006238024763480.152606192458-30.4176734414-6.21217158736-3.59769270559
34.72772443205-0.825520256834-1.06817608363.48480369956-0.1360753744714.251159486320.05156751405960.3394783287090.1177979689110.0431854495968-0.0645664347144-0.502300366552-0.08273867807020.3112180067030.0008275213742090.20388800524-0.0217709506558-0.01762980762810.235323395580.02339454621640.260668526067-23.4773597512-1.64550134029-8.33313640691
49.72035059429-3.089943825630.8758415810954.517074312620.9010337785193.33804699621-0.3685485878070.549965412598-0.498727101943-0.280486645121-0.410744209364-1.125808663150.1729584453171.359793859630.7911710341520.430302119559-0.00934891024230.1101878093980.7019947524740.1197480715820.568743071768-18.4579079732-16.8527055897-5.74496225324
56.065444800627.14900983997-2.150407703068.91015480416-1.862407334061.769554476350.560542908535-0.3921993332270.0801103623990.718069152058-0.2936916109910.8055782689670.298539884727-0.69011886717-0.2171991762130.334767234169-0.138597092922-0.02206036534890.4570833326350.0756793799470.355661797934-41.6484409928-18.81422210235.13483493167
65.277528711963.328742576740.3260269223153.25760247957-0.6179147707991.050199571930.4388644040640.0255783445251-1.646966018740.117844658073-0.381933632513-0.7516376689150.198568753921-0.0278513515819-0.03598095221630.300130568672-0.0150486707762-0.1118866260330.2687852452460.03202240809690.618064874416-31.3249306928-20.91194994941.20425476351
77.05039801501-0.4684965323283.183595204482.22104940254-0.8220381102344.079732292970.368266346115-0.677749775869-0.719254931520.40495901306-0.308073066717-0.386155972780.0842431396636-0.0891436684305-0.1053202157720.327769776668-0.113381397468-0.1118450730830.3337145825550.109475502690.364504903085-39.3123992162-22.26826200571.77370869237
80.502393262198-0.181849031743-0.5830125634290.247654890992-0.08389853882232.664450932540.0414553853121-0.240235180537-0.4157256740040.0684306846618-0.243061356842-0.3525460000380.7707686305440.3165408544160.1219461356390.867223972652-0.282156300379-0.3828992354450.8329159977580.6818659475711.01781832166-36.5410753185-30.88960971049.09462999348
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 26 )AA22 - 261 - 5
22chain 'A' and (resid 27 through 65 )AA27 - 656 - 44
33chain 'A' and (resid 66 through 103 )AA66 - 10345 - 82
44chain 'B' and (resid 1 through 10 )BB1 - 101 - 10
55chain 'B' and (resid 11 through 24 )BB11 - 2411 - 24
66chain 'B' and (resid 25 through 40 )BB25 - 4025 - 40
77chain 'B' and (resid 41 through 57 )BB41 - 5741 - 57
88chain 'B' and (resid 58 through 70 )BB58 - 7058 - 70

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