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- PDB-7s4n: Crystal structure of the tick evasin EVA-P974 complexed to human ... -

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Basic information

Entry
Database: PDB / ID: 7s4n
TitleCrystal structure of the tick evasin EVA-P974 complexed to human chemokine CCL17
Components
  • C-C motif chemokine 17
  • Evasin P974
KeywordsIMMUNE SYSTEM / Inflammation / Evasin / Chemokine / Evasion-chemokine complex
Function / homology
Function and homology information


CCR chemokine receptor binding / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / cell chemotaxis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / positive regulation of cell migration ...CCR chemokine receptor binding / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / cell chemotaxis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / positive regulation of cell migration / 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 P974 / C-C motif chemokine 17
Similarity search - Component
Biological speciesAmblyomma cajennense (Cayenne tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 9, 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
Revision 1.2Oct 16, 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 P974
C: Evasin P974
D: C-C motif chemokine 17
B: C-C motif chemokine 17


Theoretical massNumber of molelcules
Total (without water)35,5974
Polymers35,5974
Non-polymers00
Water4,089227
1
A: Evasin P974
B: C-C motif chemokine 17


Theoretical massNumber of molelcules
Total (without water)17,7982
Polymers17,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Evasin P974
D: C-C motif chemokine 17


Theoretical massNumber of molelcules
Total (without water)17,7982
Polymers17,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.431, 37.716, 69.186
Angle α, β, γ (deg.)90.000, 112.664, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 33 or (resid 34...
d_2ens_1(chain "C" and (resid 4 through 6 or (resid 7...
d_1ens_2(chain "B" and (resid 7 through 22 or (resid 23...
d_2ens_2(chain "D" and (resid 7 through 15 or (resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRASNA1 - 82
d_21ens_1TYRASNB3 - 84
d_11ens_2GLYGLUD1 - 63
d_21ens_2GLYGLUC3 - 65

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.0454549171034, 0.37818760743, -0.924612342605), (-0.704006803628, -0.668791108185, -0.238941151871), (-0.708737095795, 0.640072329662, 0.296646493061)20.7882439883, -11.5621055348, -6.51253938094
2given(0.00195288345266, 0.340614869375, -0.940200881199), (-0.634766531703, -0.726075182812, -0.264360131517), (-0.77270151836, 0.597324316989, 0.214792979069)22.0954049277, -9.82944401334, -5.25519069844

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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 C-C motif chemokine 17 / CC chemokine TARC / Small-inducible cytokine A17 / Thymus and activation-regulated chemokine


Mass: 8096.292 Da / Num. of mol.: 2
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.: 227 / 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: 1.87 Å3/Da / Density % sol: 34.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M Na3 Cit 3.5 pH (Buffer) 3 M NaCl (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: Nov 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→37.72 Å / Num. obs: 32313 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 14
Reflection shellResolution: 1.65→37.72 Å / Num. unique obs: 1514 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FPU

3fpu


Resolution: 1.65→34.03 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 1655 5.13 %
Rwork0.2079 30633 -
obs0.2094 32288 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.65 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 0 227 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512229
X-RAY DIFFRACTIONf_angle_d0.86143017
X-RAY DIFFRACTIONf_chiral_restr0.0523330
X-RAY DIFFRACTIONf_plane_restr0.0055393
X-RAY DIFFRACTIONf_dihedral_angle_d5.4047316
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.20042267396
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS1.50223860707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.34111340.33962427X-RAY DIFFRACTION97.56
1.69-1.750.34911310.31412578X-RAY DIFFRACTION99.89
1.75-1.810.35361160.27822540X-RAY DIFFRACTION99.96
1.81-1.880.26781480.25672542X-RAY DIFFRACTION99.93
1.88-1.970.26331120.23592573X-RAY DIFFRACTION100
1.97-2.070.26321630.21962509X-RAY DIFFRACTION99.89
2.07-2.20.25581710.20462516X-RAY DIFFRACTION100
2.2-2.370.25491490.20762533X-RAY DIFFRACTION99.89
2.37-2.610.25411050.21932587X-RAY DIFFRACTION100
2.61-2.990.24811410.21712564X-RAY DIFFRACTION99.96
2.99-3.770.20691410.19112606X-RAY DIFFRACTION99.96
3.77-34.030.19911440.17182658X-RAY DIFFRACTION100
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)
14.357771474270.3630501048970.5368118704467.187007451560.6290409152693.44049646812-0.3695500242010.146402902312-0.8246519888850.225641854180.0947001518675-0.493561278680.8069351032870.6301132233150.2138950347180.4138976963470.08590363823150.08608549809640.2617809767630.02614509035990.260321208211-11.13745675634.1224729703618.2111740614
26.54555276093-1.74548759771-1.018573464084.043982427290.4732304306532.9424621141-0.0465740374040.07855403370390.083952177003-0.153502723278-0.019011934618-0.2044224211280.07966095858390.2427401085940.09367570760050.226418974645-0.006537098035410.009318607443250.1758329267260.008731050012640.138734792306-17.092081998913.136322265322.7925366259
38.572017060461.160152303580.3444460619564.784638882120.3103022738662.37035898455-0.0105187259791-0.06727819223420.414731444880.196758655919-0.113562107453-0.0743684586473-0.1209827362060.005924006057170.09437994845080.2512784992130.01481959580160.003991332428760.1488534239380.02275906541010.134899884655-23.1304887619.389024260723.5097421606
48.52919453915-7.165158147116.002289040939.01974559679-2.553276156757.81339262049-0.1059678286041.060559258670.0499282569746-0.51864772984-0.512119764531.236857631090.8985101966850.6072663435560.5862494924350.893462907769-0.150831442327-0.03142349692180.449917607925-0.01773528618970.3532100409234.53744802485-8.681205219551.29648871147
53.72848098353-0.650366585231.359094881253.87853458424-0.805982961435.41962229820.1919647291260.199666887896-0.0508879306287-0.1082261945130.0341145979059-0.2061285394160.2747903842890.448362912003-0.2846053319740.1643912476480.02554725584150.05009789318310.132994332952-0.04021216672620.17506303663312.144826159-11.452194149221.0062313859
62.51570495405-0.887276131064-0.5879435384235.11739770732-1.038614091762.72382157219-0.03962316990480.250232231492-0.117775015874-0.3649606386180.07185104391280.419952810587-0.00894182471677-0.01893484367-0.05469654701260.218310929377-0.0243881173723-0.01227157478510.157147604305-0.02691762765930.2468169009664.99283690656-16.791087748517.8898453062
79.321143734972.345541539394.600076227629.250528059925.094865268726.84113511215-0.2883933378220.8931330588110.833406971774-0.5991661593890.1353140002380.435583872176-0.8339245808120.4055810215240.2166461558740.2870113960860.03107378034960.006123705689450.2280108239350.008081793369380.2633307219012.58574763258-4.5435406150127.285427635
82.268872030630.331512618126-0.1894855034854.524891855734.579292641394.53135390944-0.3210326306350.0212817717403-0.2114203316670.08392009229980.1356602059780.1480853200160.3500962456130.1765870795580.2219878226060.334109867167-0.010977205740.04319935504340.1545593904850.02776255481830.2523587390796.88531367491-16.871583795628.5833141384
95.693673408850.9509913139551.280299492317.453081201722.879904967576.40256654494-0.2497565567690.0574715126622-0.3445179839470.7344091385860.4318254238240.3264358414230.3898707594930.147694000791-0.2019971481150.255532509280.02233239238430.09124787364610.1579264609240.01727276431510.1955401355437.90433132594-15.756309089529.8174202134
103.325987678030.06587033070490.8175431380272.76232824608-3.738550021036.82358689003-0.2483557597290.01809941937850.1661825006240.0142978246985-0.2357130074170.0555612313147-0.3125350674170.3676187959920.3284425569880.3825161833510.02360287641430.01830089883550.139798422362-0.004982568345620.27289170924512.3666895026-6.712444968849.82631079405
112.58911230385-2.108706057153.067007918223.01091044119-5.121849309388.86815491333-0.1805105921360.2451890187710.3249940458030.608519018210.05890706476260.330267564355-1.54144551539-0.0979066026963-0.003012102564650.676557338980.04391465967320.07497755463450.2643949177220.0002828559151690.37756379607211.4193609393.870238208118.24213232131
124.06136732831-0.2538533597721.948644992224.31480787321-1.05806880526.239018200150.149600537053-0.003281498142960.0923250187921-0.260294117239-0.0839428507382-0.0665419033997-0.258037208218-0.0031998044359-0.1274083335170.3198625100040.04527215319170.1205552740660.137747734870.008420943287810.20033443594114.3773726355-5.3844432031311.1932420917
131.87727397804-0.6419802397190.3096052198549.35430603951.976904800950.841201979619-0.181835397801-0.005974162443270.193378456425-0.5212837788630.122451861056-0.866536079824-1.84697984636E-50.3225072621210.05380103361810.4087944222930.01447702508630.1118369340070.2706536277730.07272677599870.31370920830419.03117606836.305809805686.10002377797
142.755926075043.000296078771.581307530716.489845914110.007204246825613.167958708810.0185814672725-0.03039829020320.06692519575930.2487775121530.0707206794520.09402205509010.328262372712-0.0507040124222-0.07174407976540.364195684380.0319110195320.1119419595250.1785098687080.003297487624760.195319555953-15.3866475879-0.025709678412411.0225263208
154.23163493082.58124719643-1.249531035025.86826460113-1.720360381666.344749780370.061928882828-0.004831271078290.01929046046250.020431097739-0.168344034240.07346591684550.02030606586980.1309302559690.13735935910.268320524850.03980015934840.02562623760130.1573060973460.005066552996550.148475612024-15.23798184462.790598752210.1243268191
163.401190860375.058186747230.3335577107628.381575937451.498633099864.64980597978-0.5846805949790.679317540543-0.233249513302-0.487837038260.5419155263360.3572002514640.0801645853076-0.5751683425020.2350980693190.4120511787990.0168739740240.09188935291540.2216249610770.01749962486230.270801842901-18.147821847-5.782068034090.983591596622
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 12 )AA4 - 121 - 9
22chain 'A' and (resid 13 through 53 )AA13 - 5310 - 50
33chain 'A' and (resid 54 through 85 )AA54 - 8551 - 82
44chain 'C' and (resid 2 through 6 )CB2 - 61 - 5
55chain 'C' and (resid 7 through 21 )CB7 - 216 - 20
66chain 'C' and (resid 22 through 47 )CB22 - 4721 - 46
77chain 'C' and (resid 48 through 58 )CB48 - 5847 - 57
88chain 'C' and (resid 59 through 70 )CB59 - 7058 - 69
99chain 'C' and (resid 71 through 85 )CB71 - 8570 - 84
1010chain 'D' and (resid 5 through 20 )DC5 - 201 - 16
1111chain 'D' and (resid 21 through 29 )DC21 - 2917 - 25
1212chain 'D' and (resid 30 through 55 )DC30 - 5526 - 51
1313chain 'D' and (resid 56 through 71 )DC56 - 7152 - 67
1414chain 'B' and (resid 7 through 29 )BD7 - 291 - 23
1515chain 'B' and (resid 30 through 55 )BD30 - 5524 - 49
1616chain 'B' and (resid 56 through 69 )BD56 - 6950 - 63

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