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- PDB-7s59: Crystal structure of the tick evasin EVA-P974 complexed to a chim... -

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Basic information

Entry
Database: PDB / ID: 7s59
TitleCrystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8
Components
  • Evasin P974
  • chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
KeywordsIMMUNE SYSTEM / Inflammation / Evasin / Chemokine binder / Evasin-chemokine complex
Function / homology
Function and homology information


CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol ...CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity / exocytosis / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / neutrophil chemotaxis / response to gamma radiation / response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / regulation of cell shape / angiogenesis / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / 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 P974 / C-C motif chemokine 8 / C-C motif chemokine 7
Similarity search - Component
Biological speciesAmblyomma cajennense (Cayenne tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsBhusal, R.P. / Devkota, S.R. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases.
Authors: Bhusal, R.P. / Aryal, P. / Devkota, S.R. / Pokhrel, R. / Gunzburg, M.J. / Foster, S.R. / Lim, H.D. / Payne, R.J. / Wilce, M.C.J. / Stone, M.J.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
1: Evasin P974
3: Evasin P974
4: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
2: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4096
Polymers37,2174
Non-polymers1922
Water1629
1
1: Evasin P974
2: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7053
Polymers18,6092
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
3: Evasin P974
4: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7053
Polymers18,6092
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.240, 62.718, 53.966
Angle α, β, γ (deg.)90.000, 93.933, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
111-201-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "1" and ((resid 3 and (name N or name...
d_2ens_1(chain "3" and (resid 3 through 74 or (resid 75...
d_1ens_2(chain "2" and (resid 6 through 23 or (resid 24...
d_2ens_2(chain "4" and (resid 6 through 18 or (resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPASNA1 - 83
d_21ens_1ASPASNB2 - 84
d_11ens_2SERASPD6 - 68
d_21ens_2SERASPC1 - 63

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.843509809317, 0.528644147952, 0.0950082439671), (0.52297184824, -0.84867279638, 0.0790881194219), (0.122440383592, -0.0170249675873, -0.992329835763)15.1813088807, -3.86262324605, 47.0628960059
2given(0.862217296331, 0.493038770503, 0.116164128232), (0.487070711541, -0.869950840118, 0.0771210589675), (0.139080753041, -0.00991496635946, -0.990231406074)14.8093519999, -3.35121143455, 46.5688960808

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Components

#1: Protein Evasin P974


Mass: 9702.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amblyomma cajennense (Cayenne tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023FDY8
#2: Protein chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7 / HC14 / Monocyte chemoattractant protein 2 / Monocyte chemotactic protein 2 / MCP-2 / Small- ...HC14 / Monocyte chemoattractant protein 2 / Monocyte chemotactic protein 2 / MCP-2 / Small-inducible cytokine A8 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7


Mass: 8906.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL8, MCP2, SCYA10, SCYA8, CCL7, MCP3, SCYA6, SCYA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80075, UniProt: P80098
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS 8.5 pH (Buffer) 2 M (NH4)2SO4 (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→42.38 Å / Num. obs: 16549 / % possible obs: 98.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 7.9
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 1551 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S58

7s58


Resolution: 2.39→42.38 Å / SU ML: 0.3262 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.0284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 826 5.02 %
Rwork0.2374 15619 -
obs0.239 16445 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.98 Å2
Refinement stepCycle: LAST / Resolution: 2.39→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 10 9 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972342
X-RAY DIFFRACTIONf_angle_d1.24473186
X-RAY DIFFRACTIONf_chiral_restr0.0617357
X-RAY DIFFRACTIONf_plane_restr0.0091411
X-RAY DIFFRACTIONf_dihedral_angle_d15.8621320
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_21X-RAY DIFFRACTIONTorsion NCS0.870091873847
ens_2d_24X-RAY DIFFRACTIONTorsion NCS1.36957460104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.540.36521130.35472428X-RAY DIFFRACTION91.08
2.54-2.730.41881070.32112654X-RAY DIFFRACTION98.89
2.73-3.010.40431700.31832590X-RAY DIFFRACTION98.82
3.01-3.440.36331430.29332647X-RAY DIFFRACTION99.5
3.44-4.340.22541590.21782608X-RAY DIFFRACTION98.16
4.34-42.380.20921340.19612692X-RAY DIFFRACTION98.33
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)
11.835548625852.130078989580.8211046502912.127841272640.2880140593871.4191723494-0.05529423794030.124085575062-0.109016029220.03345189233190.281246929364-0.01212690730650.01476840675750.433561139892-0.0003847314628390.6278219387230.1086988022170.06043303514330.788309306726-0.04488669702780.4477654538357.839077252945.369318689389.79838992189
20.193671287111-0.009768263253690.1155546711670.212164191059-0.2623119548120.0154753702158-0.1361384417490.296685094812-0.4715492132820.284358481136-0.0731437915803-0.7006376072990.155614794181.01929097224-6.77763795468E-50.7094599905380.0474547924523-0.01588062810281.132116937430.01715269169380.86971796851217.08923592896.112079940086.76678614215
30.218638622649-0.0467454482077-0.1038207386440.2710123725370.006046745762260.225908812047-0.1163493996771.34555489835-0.940706574507-0.567025417895-0.0205970425432-0.4939003892170.7762511969990.6545507527440.002846616329130.734469767352-0.0734585521805-0.01073277330740.7981655260280.09401078538960.5945233453699.0966919589715.980214250811.2776802331
40.0435119407217-0.1303617363880.01472376325260.401749857872-0.02946924404210.03264223876670.08923139626240.440832567572-0.9581849162541.048509520270.232383878723-0.23798522548-0.1331107544141.902773140020.001045242072490.738122064975-0.02120058662620.1137885677560.9787068953990.05318033440070.52733194391611.508886768211.923025419420.8596365022
50.30635599595-0.2982169021960.1790447681390.4313706132450.08865907486510.212326868444-0.688774088286-0.3496913780120.05636581996290.6103080884010.580132420070.2715822174780.0787163541025-0.3566437223060.00432417523830.6153808382480.004840955317080.1027933332620.5866439113910.03890612036790.427035465372-0.6177510409613.053547222121.9611180105
60.788728833290.9793756410670.1794836814610.6666900645240.1286677388280.473186782248-0.1590666016070.6984199531921.085735369180.09378006201630.563900708054-0.35773825357-0.06166383675950.423871012101-0.0007039393216840.6874451506340.000735415080161-0.003103424680110.8204753487420.08046338352910.8719083309258.4001007122717.8792356789.03908848951
70.865069263862-1.25751022-0.05489031111241.552816011540.9407124461351.05437418223-0.2687170079590.9188128963970.00986470163612-0.3478165131360.6287879019050.422066848167-0.167474869483-0.547576602213-0.001117972720540.773955457871-0.1689562818360.005569222689040.6541962011140.05940990654270.4904556328714.1177372005617.222312498111.5132249977
80.5172884088140.417976228691-0.3346279469730.4827493492660.07501667867820.4599408591280.2117033772040.3522963428031.01651099930.59487776507-0.691058205074-1.264002700220.1140839503540.388887284343-0.003416725858270.750657339898-0.0338692845909-0.07421532957590.882098669058-0.02369959397440.95433716909427.467916908210.8864886739.622074572
90.0817778951808-0.00714301909509-0.1193329455610.195866645586-0.1573990928640.2060977990510.317797410783-0.79109885208-0.7266280779460.9841343985440.184503473303-0.7941271006461.592373614350.3301371253910.0007360096967811.02921848613-0.0399047705441-0.1775807981830.632144261099-0.1036269305181.151647246722.6656554935-8.0847274684136.8734740169
100.110860650459-0.008366891511320.006790613199070.04200278331760.05743397303230.08108296080210.6725980380550.881500339822-0.9082506546550.724753441856-0.846368935714-0.202776823511.028560641140.797802211939-0.004551151836050.7578874766980.0125792184556-0.08458085511091.16203914608-0.01414943341131.0351935109433.6858984826.5915124795739.6158678777
110.3809565212510.02734182162340.3054930860730.6061889607970.2192438812550.3579945188191.21344578494-0.0817443288454-2.185936705790.66572302564-1.005154666140.03327193161531.528249038770.7492056254580.03298699345881.047620917050.216441520217-0.3182612112720.88432248618-0.0805812965251.154801526930.8342440954-6.6974168802141.3582058584
120.193659531949-0.1313082073690.02248786725550.1178251812320.1701837050170.7792888672540.781569571679-0.101396236888-0.546473758523-0.207603241299-0.420658200566-0.106158952384-0.267918348783-0.6352260600590.0009525302371990.867029141180.237740114334-0.176767148670.921015808685-0.2138713898041.2433325351726.9845371373-7.4482247183126.1648801462
130.110783751745-0.1148080278830.01152498489510.02350926334860.1046159954380.0692270584084-0.804219672930.1894470851960.278331500660.105278171619-0.367839757275-0.245098965849-0.880683094361-0.3203219880340.0001941353069131.0673868717-0.0302682827315-0.4665866294540.875687191323-0.1288256596741.6430906830.3195264003-12.268543480537.1865459765
140.58822955619-0.539240660917-0.4877416717540.8303039229160.7917569874810.8049322623030.1067689095420.279616494811-0.7599441574670.4016925284710.2494636781170.540598125727-0.0419155259318-0.562787626176-0.0007622407937650.9031051531220.0586222528523-0.1963023373560.952787632231-0.1191064340671.4882288078928.5149736802-11.245927948536.5084850134
150.5146965313840.2066388731250.2986090439330.09134333807530.410321163033-0.21526374682-0.322081478879-0.217382187964-0.254483107044-0.06882506012940.540263979524-0.500999766777-0.1169338654880.9267604484150.002826039148260.80663116055-0.0116480547507-0.01316827327260.902944819707-0.08718095138840.92529083546120.71667841087.2579986425939.7661920429
160.431932693813-0.1255791030160.05105782332120.0169938757923-0.2518693799440.5206101889660.01633229271260.9559580045620.132847566216-0.602117743588-0.129490673032-0.967102531050.04507573707220.32104167517-0.001730007756350.701963661375-0.06756591256140.09866575365860.6716428720650.002830655457020.7517556778915.170811141515.114977776533.4302624121
17-0.0178382645483-0.08695916157110.08898003552340.308728885611-0.3968499591460.4169537345330.227908184460.733928204298-1.07192383384-0.0893900358627-0.001520226553021.27960688911-0.676434619882-0.5135759997080.001765890393170.8864630482930.04464728381310.0784061814150.9817943221510.1393318187461.1100871010614.6299742423-0.95561455142539.0574972323
181.26690969426-0.7417603849330.6957999377221.735061952070.4734798019120.733648163384-0.113962960103-0.3488679794850.434334195841-0.1191951239520.216794991002-0.6233532927520.6384182973440.677921983950.001026277447920.710258254741-0.05339615612120.007142873144060.721955872838-0.02588626284760.84643969930919.429542518112.860287328536.7861681284
190.691925788101-0.668341837483-0.147856401640.4490660395090.1267618560890.4757566108750.02265385453110.0008806960567920.2931430922510.177965453756-0.0176359394764-0.122773186707-1.225993902480.727604018663-0.0006791751318570.74155203083-0.02482517459320.05159817692340.629643475696-0.02952271334650.6734467750657.7594899566418.831367095334.3052798636
200.0599622925584-1.264894831220.5064085569530.995687534132-0.1303622788911.027629062870.1400414127590.3870034628210.1484625469980.343577625787-0.174732646725-0.2124207757950.5029964112920.1681788146110.0001076731951750.6714321137990.06973372443380.002052636733550.662999554517-0.04092247450980.6966461258734.33902317779-0.60453333672611.178410637
210.8522926944810.700171072855-0.906525598622.07687690193-0.1269061047261.317410478560.448420679753-0.182445733568-0.0909440733481-0.2601943209140.01930765477830.7809774012990.613771777352-0.338125722684-0.0001478323360330.805885152730.0715049378636-0.1108678759740.7751822691340.0005800415790350.7668879283246.56788405325-7.2150505727311.0078847982
221.639874890840.104569990306-0.530871135762-0.03347538633940.01528351071780.1409135671550.914777178963-0.759855374681-0.839578392588-0.0363517896905-0.710334820888-1.79479530362-0.4620951262840.5701778151220.01742873143021.507701752780.222250920722-0.8448270862240.37720289586-0.002695936448841.742127275124.53299005083-17.2169000298.29467583687
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain '1' and (resid 3 through 26 )1A3 - 261 - 24
22chain '1' and (resid 27 through 41 )1A27 - 4125 - 39
33chain '1' and (resid 42 through 47 )1A42 - 4740 - 45
44chain '1' and (resid 48 through 53 )1A48 - 5346 - 51
55chain '1' and (resid 54 through 59 )1A54 - 5952 - 57
66chain '1' and (resid 60 through 70 )1A60 - 7058 - 68
77chain '1' and (resid 71 through 85 )1A71 - 8569 - 83
88chain '3' and (resid 2 through 12 )3B2 - 121 - 11
99chain '3' and (resid 13 through 26 )3B13 - 2612 - 25
1010chain '3' and (resid 27 through 36 )3B27 - 3626 - 35
1111chain '3' and (resid 37 through 47 )3B37 - 4736 - 46
1212chain '3' and (resid 48 through 59 )3B48 - 5947 - 58
1313chain '3' and (resid 60 through 68 )3B60 - 6859 - 67
1414chain '3' and (resid 69 through 85 )3B69 - 8568 - 84
1515chain '4' and (resid 6 through 21 )4C6 - 211 - 16
1616chain '4' and (resid 22 through 30 )4C22 - 3017 - 25
1717chain '4' and (resid 31 through 40 )4C31 - 4026 - 35
1818chain '4' and (resid 41 through 57 )4C41 - 5736 - 52
1919chain '4' and (resid 58 through 76 )4C58 - 7653 - 71
2020chain '2' and (resid 1 through 21 )2D1 - 211 - 21
2121chain '2' and (resid 22 through 57 )2D22 - 5722 - 57
2222chain '2' and (resid 58 through 68 )2D58 - 6858 - 68

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