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- PDB-7scu: Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Hum... -

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Basic information

Entry
Database: PDB / ID: 7scu
TitleCrystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL7
Components
  • C-C motif chemokine 7
  • Evasin P1243
KeywordsIMMUNE SYSTEM / Inflammation / Chemokine / Ticks / Evasin
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: 1.86 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) Australia
CitationJournal: To Be Published
Title: Crystal Structure of Tick Evasin EVA-AAM1001 complexed to human chemokine CCL7
Authors: Devkota, S.R. / Bhusal, R.P. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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 P1243
B: C-C motif chemokine 7


Theoretical massNumber of molelcules
Total (without water)20,0892
Polymers20,0892
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.258, 71.258, 66.418
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: 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.: 90 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Acet 4.6 pH (Buffer),2 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: 0.953 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.86→48.59 Å / Num. obs: 14877 / % possible obs: 99.8 % / Redundancy: 25.4 % / Biso Wilson estimate: 30.93 Å2 / CC1/2: 0.996 / Net I/σ(I): 20
Reflection shellResolution: 1.86→1.9 Å / Num. unique obs: 912 / CC1/2: 0.67

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Processing

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

7scs


Resolution: 1.86→40.14 Å / SU ML: 0.1895 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2102 665 4.49 %
Rwork0.193 14159 -
obs0.1938 14824 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.32 Å2
Refinement stepCycle: LAST / Resolution: 1.86→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 90 1214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391146
X-RAY DIFFRACTIONf_angle_d0.66891556
X-RAY DIFFRACTIONf_chiral_restr0.0441180
X-RAY DIFFRACTIONf_plane_restr0.0059200
X-RAY DIFFRACTIONf_dihedral_angle_d5.485160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-2.010.241540.23442731X-RAY DIFFRACTION99.35
2.01-2.210.22631270.20092787X-RAY DIFFRACTION100
2.21-2.530.21891250.19952806X-RAY DIFFRACTION100
2.53-3.190.25741270.20862841X-RAY DIFFRACTION100
3.19-40.140.1851320.17832994X-RAY DIFFRACTION99.78
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)
14.92173185216-0.407624224895-4.758361546812.6418955152-0.6717066589035.126676803760.409879001581-1.648667228341.127453020871.344701376140.2946926711952.11815455224-0.301105206531-2.16522981246-0.7276289967890.664899918225-0.03055666623480.0296488603550.7883416408270.02904879100460.67983403761-8.7426950249724.35909847630.650436553951
23.528025367680.8255480594930.1226041851062.1776170774-1.436398090533.174092681630.0915402029410.263468783013-0.194129117656-0.07465392117960.0921021629398-0.06795141677380.111525890475-0.0279013297024-0.185935545820.1954690487570.0254309134479-0.01965056615220.217668541926-0.03689653715520.176522802595.7940428894328.7598928611-5.15968948793
35.22436106012-0.604508506834-1.817751767634.006650451761.222156947546.27439775955-0.009136543860480.543856205755-0.0868700584078-0.1318432306730.0440840173985-0.321958301868-0.152478652310.355803509738-0.02132126815990.18235912302-0.0381519982433-0.005790690253990.2642007638710.006147946129090.21289212051312.859127590434.527635751-10.1128180018
48.660080941426.6886432134-5.00364220617.00704651278-5.378534078494.342024006370.2327424828160.3584285261260.03955918006550.2035583244720.004131862908730.422658369782-0.214918071452-0.514946187404-0.05250742241610.238217491199-0.0200244382798-0.0561005843580.320918022405-0.02644095940980.3073542801040.72079012117920.04197576831.90078995041
52.16905209938-1.06446947124-4.007953955076.950906034580.05254657001627.884632732770.0405704939507-0.125998585349-1.1464839564-0.661065453283-0.1602166736650.05341200438520.4912253076760.1415252933530.09239398999570.387721723901-0.0744057050583-0.0136089026850.3898983965990.03100022597070.57225174209-1.94322409298.789426481552.86922716722
68.885884366633.6486029404-0.7021354451536.09910929958-0.1737838543853.28316063278-0.05542231798870.11929812299-0.7165157154430.1603096370220.0651630940163-0.7057578733510.2732624302790.202843668197-0.05504766879350.2558033066990.0119044341268-0.05623974804380.221234724241-0.001731397390930.2638640156066.6054843162917.1625530861.38590362893
72.597590778832.008121745260.8631678601589.61820198993-0.008541852725585.231459893110.142255775516-0.141546521043-0.3524839032540.405452988794-0.01412989413820.01239583906290.05907311946440.175355326012-0.3963257650590.2509707288-0.00307819849503-0.05643539229490.3319551241060.03540826765390.318720593211-2.5654354690614.77192124212.9036408696
87.37071552012-1.19589651271-0.2244584517012.130985523411.291995705676.75548974498-0.293316760591-0.770484863446-1.104813202571.14868737386-0.42899731492-0.8300893045640.398160247532-0.3451957201770.5082330201090.407289645922-0.0772005125228-0.02746939829720.4940486397910.248276968370.6417216557240.3080600248457.8391204233410.689337525
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 22 )AA17 - 221 - 6
22chain 'A' and (resid 23 through 63 )AA23 - 637 - 47
33chain 'A' and (resid 64 through 101 )AA64 - 10148 - 85
44chain 'B' and (resid 7 through 21 )BB7 - 211 - 15
55chain 'B' and (resid 22 through 30 )BB22 - 3016 - 24
66chain 'B' and (resid 31 through 45 )BB31 - 4525 - 39
77chain 'B' and (resid 46 through 57 )BB46 - 5740 - 51
88chain 'B' and (resid 58 through 69 )BB58 - 6952 - 63

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