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- PDB-8fk9: Crystal Structure of the Tick Evasin EVA-ACA1001 Complexed to Hum... -

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Basic information

Entry
Database: PDB / ID: 8fk9
TitleCrystal Structure of the Tick Evasin EVA-ACA1001 Complexed to Human Chemokine CCL16
Components
  • C-C motif chemokine 16
  • Evasin P991
KeywordsCYTOKINE / Evasin / Chemokine-binding protein / ticks
Function / homology
Function and homology information


negative regulation of chemokine activity / CCR chemokine receptor binding / cell communication / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / chemoattractant activity / antimicrobial humoral immune response mediated by antimicrobial peptide ...negative regulation of chemokine activity / CCR chemokine receptor binding / cell communication / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / chemoattractant activity / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cell-cell signaling / G alpha (i) signalling events / positive regulation of cell migration / inflammatory response / 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 P991 / C-C motif chemokine 16
Similarity search - Component
Biological speciesAmblyomma cajennense (Cayenne tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Protein Sci. / Year: 2024
Title: Structural basis of chemokine recognition by the class A3 tick evasin EVA-ACA1001.
Authors: Devkota, S.R. / Aryal, P. / Wilce, M.C.J. / Payne, R.J. / Stone, M.J. / Bhusal, R.P.
History
DepositionDec 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: 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 P991
B: Evasin P991
C: C-C motif chemokine 16
D: C-C motif chemokine 16


Theoretical massNumber of molelcules
Total (without water)46,7974
Polymers46,7974
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.062, 122.801, 60.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
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
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11D-207-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 21 through 23 or (resid 24...
d_2ens_1(chain "B" and (resid 21 through 49 or (resid 50...
d_1ens_2(chain "C" and (resid 15 through 27 or (resid 28...
d_2ens_2(chain "D" and (resid 15 through 19 or (resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUPROA2 - 85
d_21ens_1GLUPROB1 - 84
d_11ens_2SERPROC2 - 64
d_21ens_2SERPROD1 - 63

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.131049038746, -0.991373683561, 0.00209021230146), (-0.991373784249, 0.131052812078, 0.00178335357221), (-0.00204189799992, -0.0018384749078, -0.999996225324)63.4900385083, 55.6943202119, 30.2147994612
2given(-0.127897899322, -0.991785898461, -0.00169084684754), (-0.991215310092, 0.127881840943, -0.0337408327606), (0.0336799107419, -0.00263938834914, -0.999429185706)63.5334656577, 56.0416954586, 29.3317394086

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Components

#1: Protein Evasin P991


Mass: 11940.115 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: A0A023FFD0
#2: Protein C-C motif chemokine 16 / Chemokine CC-4 / HCC-4 / Chemokine LEC / IL-10-inducible chemokine / LCC-1 / Liver-expressed ...Chemokine CC-4 / HCC-4 / Chemokine LEC / IL-10-inducible chemokine / LCC-1 / Liver-expressed chemokine / Lymphocyte and monocyte chemoattractant / LMC / Monotactin-1 / MTN-1 / NCC-4 / Small-inducible cytokine A16


Mass: 11458.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL16, ILINCK, NCC4, SCYA16 / Production host: Escherichia coli (E. coli) / References: UniProt: O15467
#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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES 7 pH, 0.5 %v/v Jeff ED-2001, 1.1 M Na2 Malon

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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: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.7→49.24 Å / Num. obs: 23069 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 47.18 Å2 / CC1/2: 0.987 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 1609 / CC1/2: 0.592

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.37 Å / SU ML: 0.2779 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2661 1079 4.68 %
Rwork0.2528 21990 -
obs0.2534 23069 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 43 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412233
X-RAY DIFFRACTIONf_angle_d0.72363080
X-RAY DIFFRACTIONf_chiral_restr0.0491371
X-RAY DIFFRACTIONf_plane_restr0.0057396
X-RAY DIFFRACTIONf_dihedral_angle_d11.1566315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.623855966542
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.581083839448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.33211220.35092782X-RAY DIFFRACTION99.9
2.82-2.970.27951480.33452718X-RAY DIFFRACTION99.76
2.97-3.160.2951370.30132767X-RAY DIFFRACTION99.42
3.16-3.40.31141320.27542736X-RAY DIFFRACTION99.31
3.4-3.740.2371190.27492732X-RAY DIFFRACTION99.55
3.74-4.280.27361450.22552766X-RAY DIFFRACTION99.73
4.29-5.40.22591070.19852767X-RAY DIFFRACTION99.69
5.4-42.370.25441690.23272722X-RAY DIFFRACTION99.18
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)
14.189983639-1.6091466893-0.7950262677794.492407957160.9617167762454.913821502790.116860409582-0.003761466950620.400017575991-0.1609999109550.236545123768-0.0597365586253-1.040895667970.311713577513-0.437987388330.566572219993-0.0488724650895-0.01212926697710.3869376701930.04370315367130.34338404051223.41850.612.558
28.63321927415-0.465089668067-2.319263439647.796278610538.61031423819.81552281209-0.413550879815-0.2653788743120.8229627311130.2065534209360.4370343888040.735900128244-0.239134574226-0.464596039621-0.02342640617710.6621637341720.130515062285-0.01391103310120.3708139521170.08660158057420.76748011399214.00146.3793.176
35.523648165315.55357132823-2.075104195877.11230219161.600246323418.597326178190.08055712200321.051730949221.64173650695-1.99753619276-0.1194426135211.06735565651-1.0230900187-0.676824852792-0.009723326864841.107830350760.283203177325-0.02840202221210.4742218564140.1487111594210.60721313114216.7856.086-4.516
45.46481179856-0.732276376354-0.8523361520651.64323407785-0.1929159480635.52796124013-0.2050531423890.1542569545360.5910908230350.3850393858240.5505780295310.469823207121-0.310979727025-0.941086708139-0.4421287347870.4254038687640.008396527018680.1069361424970.4150944263310.06641107814990.58266290880313.00939.51422.597
56.337801737780.6744714192774.991573592167.76587257322-1.176133973165.980511508040.7324007781510.5160890681270.0527231250211-0.570073782729-0.342864405874-0.1229221246781.260880433490.739169464154-0.2341000700710.606040488130.1460507056460.02701698951710.4585962594060.02058211864060.2827286165268.82441.35231.128
67.32968554602-1.781581280381.234372048574.25471268408-0.9024581092732.079505801650.232628626614-0.645942828555-0.5780126308180.637003877456-0.07507356638070.2798910023380.446409217997-0.319245377234-0.2691617328920.556533754904-0.03488569781310.06883451258370.3984793584380.03615508119460.31764919295412.5437.22927.127
72.43595317366-2.527455423042.92485628899.53761779188-0.8310453021264.51450536356-0.667963321168-0.1256362334790.3820088249030.509874569955-0.07600639770660.98981870132-0.0795720540477-0.7664239703910.3734747050230.3903077389780.1105406791220.02496280874320.429266778474-0.02326283069740.5268165965415.5848.26826.966
88.738553407926.2599916256-3.967272639337.10985520094-6.680809213789.402978948610.367155047196-0.9905430887150.6793703084211.583398293540.276746411961.85954817079-1.365807124450.682203048955-0.5791708451880.856428858143-0.1460886551470.283987384450.735988627312-0.1366743120010.632314722065.64645.9834.377
93.70556536761-2.3158000677-1.12814664696.319253853843.606157303352.244321849680.516913930443-0.7721908451332.169038692120.3982899139920.911454424909-0.559373430086-1.44748476554-1.41544282968-1.38751930590.9262336111260.1236424006920.2600476597580.800256895869-0.01498480140170.72222462534527.18749.55212.942
105.9138408653-0.153799997579-0.213061102227.131942100253.968023001334.059561800430.1830442874770.500563791575-0.0176784768878-0.6997822321950.173518557413-0.404874376318-1.097336558530.122516363743-0.4448422265430.577033417363-0.104350380055-0.003984526828070.4376265156080.08779837060650.33833141469836.22339.377-0.167
114.61170881028-0.896474330587-1.267772636128.721309406593.198546779432.493636821680.353991260667-0.9175027793930.3188652854230.956589192451-0.566581254169-0.239135355808-0.2200675045150.2316518167150.2272254544590.682115472139-0.09129171524570.0302613597920.542116929239-0.04756899502370.31541233767337.8137.8687.342
121.02752416458-1.334724862310.5258367364699.59696763974-3.774795343647.802771942390.684701882725-0.1063510566340.022105194078-0.38140795096-0.839910484323-0.85851433446-1.093203028991.86736346141-0.0873898374040.514048660876-0.04398041106670.0684003681520.6160069016790.00683780660180.55286863870545.62236.363-3.747
132.836991490071.66030743421-2.147398029741.492958438270.7169773561358.61099293179-0.02653251842430.4722763861330.2279976481270.4361849498810.203792453639-0.0718849091077-0.295105571483-0.405850738956-0.1102717526210.3917458696390.06903308140240.02664291247550.373762493183-0.02944590534830.36634930232340.6133.276-0.967
145.26116887312.68687180159-2.070877834174.56724421134-4.353539990644.21772089227-0.4390399615090.521428764281-0.0739372019959-1.4778516327-1.05507357525-0.3556042104220.8492372898080.7351066680121.091708364491.131183645920.381301484743-0.2286570919170.7954096145490.03234138206740.61793015532511.12935.01115.369
155.833230702740.4332994889480.5519082971355.67508474247-0.7129386160467.027396780080.263921406249-0.392638374436-0.1260198654570.644836837488-0.0931794798865-0.161111287079-0.266696767078-0.614929427292-0.09016919411270.519087405762-0.1472809447850.0375617396790.362081837826-0.01830475376760.36336640284418.7826.21126.173
167.80051253735-0.823181227133-2.565051459625.691682417281.9608155137.19380718027-0.320757388792-0.630877579065-1.25605889857-0.608559036173-0.267274404167-0.05865305315011.5650316525-0.8228325722470.3871218921110.643930153293-0.12404909886-0.07215098617690.4942024567860.1037831653860.49479287868522.01615.93632.695
172.926782495431.18185229815-4.438002682091.62311176966-0.3215568190347.900387580140.0912653927252-0.471373431276-0.1043946095191.445790689390.03646424825050.13672845848-0.3114197562540.313296790164-0.0927575673860.8262665082540.04491942010950.0579019243970.3554562281880.02088305168240.3986470727225.32219.68530.99
187.00722813162-2.24776432318-2.68535517023.13203866564.342769639825.74542982261-0.219611933630.6247915168130.8867753762870.413892624441-0.254084000845-0.31661993222-0.836503621946-0.221224990472-0.02551499704770.811620970083-0.053061649386-0.1064868428820.331905999640.1519951768080.55330984725824.0446.1566.295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 28:57 )C28 - 57
2X-RAY DIFFRACTION2( CHAIN C AND RESID 58:68 )C58 - 68
3X-RAY DIFFRACTION3( CHAIN C AND RESID 69:77 )C69 - 77
4X-RAY DIFFRACTION4( CHAIN D AND RESID 15:30 )D15 - 30
5X-RAY DIFFRACTION5( CHAIN D AND RESID 31:37 )D31 - 37
6X-RAY DIFFRACTION6( CHAIN D AND RESID 38:57 )D38 - 57
7X-RAY DIFFRACTION7( CHAIN D AND RESID 58:69 )D58 - 69
8X-RAY DIFFRACTION8( CHAIN D AND RESID 70:77 )D70 - 77
9X-RAY DIFFRACTION9( CHAIN A AND RESID 20:28 )A20 - 28
10X-RAY DIFFRACTION10( CHAIN A AND RESID 29:49 )A29 - 49
11X-RAY DIFFRACTION11( CHAIN A AND RESID 50:66 )A50 - 66
12X-RAY DIFFRACTION12( CHAIN A AND RESID 67:87 )A67 - 87
13X-RAY DIFFRACTION13( CHAIN A AND RESID 88:104 )A88 - 104
14X-RAY DIFFRACTION14( CHAIN B AND RESID 21:25 )B21 - 25
15X-RAY DIFFRACTION15( CHAIN B AND RESID 26:60 )B26 - 60
16X-RAY DIFFRACTION16( CHAIN B AND RESID 61:87 )B61 - 87
17X-RAY DIFFRACTION17( CHAIN B AND RESID 88:104 )B88 - 104
18X-RAY DIFFRACTION18( CHAIN C AND RESID 14:27 )C14 - 27

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