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- PDB-7so0: Crystal Structure of the Engineered Tick Evasin EVA-P974(F31A) Co... -

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Basic information

Entry
Database: PDB / ID: 7so0
TitleCrystal Structure of the Engineered Tick Evasin EVA-P974(F31A) Complexed to Human Chemokine CCL2
Components
  • C-C motif chemokine 2
  • Evasin P974
KeywordsIMMUNE SYSTEM / Inflammation / Chemokine / Tick Evasin
Function / homology
Function and homology information


helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / lymphocyte chemotaxis ...helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / lymphocyte chemotaxis / cellular homeostasis / positive regulation of endothelial cell apoptotic process / C-C chemokine binding / NFE2L2 regulating inflammation associated genes / eosinophil chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / negative regulation of vascular endothelial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of calcium ion import / positive regulation of nitric-oxide synthase biosynthetic process / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / cell surface receptor signaling pathway via JAK-STAT / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / humoral immune response / cellular response to interleukin-1 / sensory perception of pain / cytoskeleton organization / viral genome replication / positive regulation of synaptic transmission, glutamatergic / neutrophil chemotaxis / animal organ morphogenesis / response to bacterium / cytokine-mediated signaling pathway / cellular response to type II interferon / chemotaxis / positive regulation of T cell activation / cellular response to tumor necrosis factor / regulation of cell shape / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signaling receptor binding / 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 2
Similarity search - Component
Biological speciesAmblyomma cajennense (Cayenne tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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
DepositionOct 28, 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
A: Evasin P974
B: C-C motif chemokine 2


Theoretical massNumber of molelcules
Total (without water)18,2992
Polymers18,2992
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-11 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.785, 36.785, 108.682
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Evasin P974


Mass: 9625.984 Da / Num. of mol.: 1 / Mutation: F31A
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 2 / HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / ...HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / Monocyte chemotactic protein 1 / MCP-1 / Monocyte secretory protein JE / Small-inducible cytokine A2


Mass: 8673.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL2, MCP1, SCYA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13500
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M Na3 Cit 3.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953731894493 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731894493 Å / Relative weight: 1
ReflectionResolution: 1.74→31.86 Å / Num. obs: 33772 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 27.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 31.07
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 913 / CC1/2: 0.994

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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: 1.74→31.86 Å / SU ML: 0.141 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 29.4353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2017 1589 4.71 %
Rwork0.1844 32183 -
obs0.1853 33772 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.33 Å2
Refinement stepCycle: LAST / Resolution: 1.74→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 0 129 1288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741181
X-RAY DIFFRACTIONf_angle_d1.11911604
X-RAY DIFFRACTIONf_chiral_restr0.0495182
X-RAY DIFFRACTIONf_plane_restr0.0074207
X-RAY DIFFRACTIONf_dihedral_angle_d5.5727162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.29521400.25262872X-RAY DIFFRACTION99.01
1.79-1.860.21241480.23712928X-RAY DIFFRACTION99.87
1.86-1.930.26281920.21142927X-RAY DIFFRACTION99.97
1.93-2.020.25681640.19952885X-RAY DIFFRACTION100
2.02-2.130.24891100.17452978X-RAY DIFFRACTION100
2.13-2.260.22851280.19712969X-RAY DIFFRACTION99.97
2.26-2.430.21541600.22752942X-RAY DIFFRACTION100
2.44-2.680.22911080.23282945X-RAY DIFFRACTION99.9
2.68-3.070.23411230.19492968X-RAY DIFFRACTION99.84
3.07-3.860.16591120.16612919X-RAY DIFFRACTION99.77
3.86-31.860.17752040.15142850X-RAY DIFFRACTION98.39
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)
13.759802980451.730789304280.6974916587754.119727382881.437491405643.863331642640.0209000116810.0632171691941-0.394427233574-0.1556136572680.0290939516286-0.4326587252940.247631706320.219019880927-0.04890795010730.2469131819880.04832036091610.02299024373210.1831535324420.03065605847690.18099909990221.1253199268-14.9057862542-14.3773842405
27.949073767360.890664883789-2.296381917555.447766457352.167574947156.514594380420.198606278897-0.168609526838-0.1952170604320.178346397531-0.218896320342-0.116291121524-0.2399153339170.1527450966720.01982158410660.3011188749350.013263942383-0.02441648085470.2277167097770.04065316740.14445823483621.3595334589-5.67089242014-4.57827408269
31.680799988271.683484359871.581280128487.837359268064.675174849088.72510011987-0.185445296846-0.0608745134306-0.1743088277030.0112453657283-0.1767683560950.09431070556740.178524075788-0.09545189215090.3891578554930.2433163162110.01127803083460.03721736852220.1559747117820.01756975144790.2288660036914.6603184227-17.5772396175-20.4571399478
43.829479482330.298352773769-0.7752904135346.96419837245-0.3903732355954.7710092505-0.0690644589184-0.0832470651486-0.08076575280240.6566413147630.04011585014440.7636011765960.661438399842-0.606387617386-0.07187723524180.301231071592-0.0342269154160.07217487743650.2929060949490.008524503493130.2749469869155.39690161037-23.6648090355-20.3326376038
54.569375072422.901609282061.930148795332.902255383023.182419012214.45096539549-0.158132652763-0.09756159331430.5448142150460.0362217938116-0.194994535250.771741158008-0.328270295799-0.3361257514310.3168484726310.2392589841550.03082261692850.013579179970.2029858245730.003585322489390.23482968104110.2918629009-12.9060415527-19.3967611418
67.11056512711.718814923770.05861904524284.31807682842-0.1219950783163.32936494415-0.08639319747220.163852017603-0.14182197639-0.02781798890830.08141674655710.4032688191650.180819379172-0.499054554396-0.01259154529720.257850493926-0.01378874418260.03507168606550.182916464886-0.01200752118320.1927824722323.23834108704-23.3296677831-23.9660933032
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 41 )AA2 - 411 - 40
22chain 'A' and (resid 42 through 85 )AA42 - 8541 - 84
33chain 'B' and (resid 7 through 21 )BB7 - 211 - 15
44chain 'B' and (resid 22 through 31 )BB22 - 3116 - 25
55chain 'B' and (resid 32 through 45 )BB32 - 4526 - 39
66chain 'B' and (resid 46 through 76 )BB46 - 7640 - 70

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