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

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Basic information

Entry
Database: PDB / ID: 7sct
TitleCrystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL16
Components
  • C-C motif chemokine 16
  • Evasin P1243
KeywordsIMMUNE SYSTEM / Inflammation / Chemokine / Ticks / Evasins
Function / homology
Function and homology information


negative regulation of chemokine activity / chemokine binding / CCR chemokine receptor binding / cell communication / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / chemoattractant activity ...negative regulation of chemokine activity / chemokine binding / 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 P1243 / C-C motif chemokine 16
Similarity search - Component
Biological speciesAmblyomma americanum (Lone Star tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
Citation
Journal: Nat Commun / Year: 2023
Title: Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins.
Authors: Devkota, S.R. / Aryal, P. / Pokhrel, R. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R.J. / Wilce, M.C.J. / Bhusal, R.P. / Stone, M.J.
#1: Journal: Res Sq / Year: 2023
Title: Engineering Broad-spectrum Inhibitors of Inflammatory Chemokines from a New Family of Tick Evasins
Authors: Devkota, S. / Aryal, P. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R. / Wilce, M. / Bhusal, R. / Stone, M.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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 16


Theoretical massNumber of molelcules
Total (without water)22,5732
Polymers22,5732
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-13 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.258, 96.258, 84.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-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 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.: 1
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.: 79 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.26 M (NH4)2SO4 (Precipitant),0.1 M HEPES 7.5 pH (Buffer)

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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: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.84→48.13 Å / Num. obs: 17690 / % possible obs: 99.9 % / Redundancy: 26 % / Biso Wilson estimate: 35.19 Å2 / CC1/2: 0.999 / Net I/σ(I): 23
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 1051 / CC1/2: 0.829

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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: 1.84→38.38 Å / SU ML: 0.2094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2101 890 5.04 %
Rwork0.2031 16772 -
obs0.2035 17662 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.26 Å2
Refinement stepCycle: LAST / Resolution: 1.84→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 79 1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721196
X-RAY DIFFRACTIONf_angle_d1.08311631
X-RAY DIFFRACTIONf_chiral_restr0.0583187
X-RAY DIFFRACTIONf_plane_restr0.0077209
X-RAY DIFFRACTIONf_dihedral_angle_d6.0096166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.950.29491440.2912733X-RAY DIFFRACTION99.41
1.95-2.10.26911430.23732755X-RAY DIFFRACTION99.9
2.1-2.310.26631370.21632759X-RAY DIFFRACTION99.59
2.31-2.650.26861570.22492772X-RAY DIFFRACTION99.86
2.65-3.340.20841550.22122809X-RAY DIFFRACTION99.87
3.34-38.380.17861540.17822944X-RAY DIFFRACTION99.71
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)
13.408309130360.9026349685423.422651898599.937031712073.448748995874.116880251590.384527171569-1.62418192437-0.6193260455470.5103380279650.134220274683-0.1483993514141.339900694040.0321418019482-0.469493263980.652119932575-0.00435675018886-0.02807217834810.9059367000180.1024660425720.819640839699-10.553493695313.8518078508-6.22457261598
27.09116535070.7312557247142.191620884884.157486675712.616131512068.11065371457-0.06146090172960.50496481696-0.464095728699-0.4928923815540.146386312121-0.398493039815-0.0212524173190.589098999427-0.128604965470.34710840093-0.005320430947540.09571893828060.255534758792-0.03483799423330.389492407033-18.084736553213.8449873973-26.0536211834
34.443805420780.7134821141971.024210161375.89604994635-0.820461605785.061567418920.01719316849330.649238891559-0.682414320364-0.777933180542-0.0147615807940.04524073496960.112542348360.2434858642130.04103999352490.3814828825990.02442906353310.05001013424140.31255672695-0.1241487272440.439674944319-22.29893735698.84406672444-29.2281480569
44.97774422798-3.308242791012.0065294797E-54.36493629966-0.4544522238966.225701087550.4694302445860.541298888246-0.193132496709-0.626897588761-0.3897123116580.13151991191-0.2017167228110.0946100540957-0.08474237476060.453971721980.0092924037439-0.01041418911990.335531094347-0.05476890289240.402274975942-26.242135494511.4925101157-31.1091062
58.005982331090.5706778810373.997300993723.263155728311.517731676843.25819813773-0.0880677091178-0.4226308652650.132324044994-0.0253961956204-0.05960686122830.02567010639580.0594791056332-0.4921746775190.08858916720080.3772510709030.01059685361260.1026633456240.420580859329-0.0571088456940.445089807453-13.310629280220.4025448513-14.3420988941
68.79237396773-2.847541475656.157459663074.45857851902-3.711165182247.28044279962-0.02314804162160.07597217086120.4973961980280.0508377274482-0.252101141201-0.275156276772-0.468580520020.2222446471780.1770359896950.359520485665-0.03125965117190.01213185594260.371453876273-0.04786137660820.443147992146-2.8197092551124.3122411207-14.1686991914
76.04790277074-0.2306288957063.719505715091.209019054150.6533054609843.76216630902-0.246325134896-0.03887546827630.244606523226-0.19537895177-0.1069496658810.00236305575429-0.2296636609630.01829510578650.2843694450850.3782481034740.036678383570.029621696310.355337900125-0.04964005510760.492491279322-12.628353258123.318667847-19.7030068912
84.82380147747-4.555626073935.844690545424.43055141005-5.682936588638.36459212113-0.143418236085-0.181578989846-1.38637932531-0.3970937014720.0745046846196-0.2782563875790.6992789280570.00804140955896-0.001000620012960.4077159595440.04884014120150.06216646945450.416951534021.35539816928E-60.729598024592-4.7807471968916.5992049461-13.5460913913
99.046816486510.1568292585670.5072391711416.81550155927-0.7402567785824.38906213784-0.174422254486-0.7642025973881.330014883210.124932676090.0819875766447-0.383909141192-0.3559882314580.2158033768520.04432733077230.38602942924-0.015432864577-0.006207386664830.384608091078-0.1438252787040.467699791393-6.0288735200629.9979602288-14.4680179243
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 21 )AA15 - 211 - 7
22chain 'A' and (resid 22 through 46 )AA22 - 468 - 32
33chain 'A' and (resid 47 through 84 )AA47 - 8433 - 70
44chain 'A' and (resid 85 through 100 )AA85 - 10071 - 86
55chain 'B' and (resid 14 through 27 )BB14 - 271 - 14
66chain 'B' and (resid 28 through 37 )BB28 - 3715 - 24
77chain 'B' and (resid 38 through 49 )BB38 - 4925 - 36
88chain 'B' and (resid 50 through 57 )BB50 - 5737 - 44
99chain 'B' and (resid 58 through 79 )BB58 - 7945 - 66

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