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- PDB-7p8x: Crystal Structure of leukotoxin LukE from Staphylococcus aureus i... -

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Basic information

Entry
Database: PDB / ID: 7p8x
TitleCrystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a doubly sulfated CCR2 N-terminal peptide
Components
  • C-C chemokine receptor type 2
  • Leucotoxin LukEv
KeywordsTOXIN / leukotoxin / beta barrel pore forming toxin / cytolysis / hemolysis
Function / homology
Function and homology information


T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / positive regulation of thymocyte migration ...T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / positive regulation of thymocyte migration / positive regulation of hematopoietic stem cell migration / monocyte extravasation / CCR2 chemokine receptor binding / negative regulation of type 2 immune response / regulation of vascular endothelial growth factor production / positive regulation of NMDA glutamate receptor activity / Beta defensins / macrophage migration / positive regulation of monocyte extravasation / regulation of macrophage migration / regulation of T cell cytokine production / neutrophil clearance / chemokine receptor activity / positive regulation of leukocyte tethering or rolling / positive regulation of T-helper 1 type immune response / inflammatory response to wounding / positive regulation of T cell chemotaxis / cytolysis in another organism / positive regulation of alpha-beta T cell proliferation / negative regulation of adenylate cyclase activity / cellular homeostasis / C-C chemokine receptor activity / C-C chemokine binding / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / dendritic cell chemotaxis / regulation of T cell differentiation / Interleukin-10 signaling / monocyte chemotaxis / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / hemopoiesis / blood vessel remodeling / cellular defense response / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of interleukin-2 production / negative regulation of angiogenesis / positive regulation of synaptic transmission, glutamatergic / cell chemotaxis / calcium-mediated signaling / fibrillar center / cytokine-mediated signaling pathway / response to wounding / intracellular calcium ion homeostasis / positive regulation of inflammatory response / chemotaxis / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of T cell activation / positive regulation of cold-induced thermogenesis / toxin activity / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / perikaryon / inflammatory response / immune response / external side of plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CC chemokine receptor 2 / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Chemokine receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...CC chemokine receptor 2 / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Chemokine receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
IMIDAZOLE / C-C chemokine receptor type 2 / Leucotoxin LukEv
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLambey, P. / Hoh, F. / Peysson, F. / Granier, S. / Leyrat, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE15-0002-01 France
CitationJournal: Elife / Year: 2022
Title: Structural insights into recognition of chemokine receptors by Staphylococcus aureus leukotoxins.
Authors: Lambey, P. / Otun, O. / Cong, X. / Hoh, F. / Brunel, L. / Verdie, P. / Grison, C.M. / Peysson, F. / Jeannot, S. / Durroux, T. / Bechara, C. / Granier, S. / Leyrat, C.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Leucotoxin LukEv
M: C-C chemokine receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7665
Polymers35,5042
Non-polymers2613
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-19 kcal/mol
Surface area13250 Å2
Unit cell
Length a, b, c (Å)63.298, 72.411, 79.001
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucotoxin LukEv / Variant of LukE


Mass: 34686.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lukEv, SAOUHSC_01955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FXB0
#2: Protein/peptide C-C chemokine receptor type 2 / C-C CKR-2 / CC-CKR-2 / CCR-2 / CCR2 / Monocyte chemoattractant protein 1 receptor / MCP-1-R


Mass: 817.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P41597
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.4→49.4 Å / Num. obs: 72136 / % possible obs: 99.2 % / Redundancy: 4.1 % / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 3432 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8T

7p8t


Resolution: 1.4→40.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 3616 -RANDOM
Rwork0.1865 ---
obs0.1871 71406 99 %-
Displacement parametersBiso mean: 33.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.5416 Å20 Å20 Å2
2---2.5493 Å20 Å2
3---4.0909 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.4→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 15 295 2607
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.213453HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d878SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes453HARMONIC5
X-RAY DIFFRACTIONt_it2527HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion321SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies20HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2472SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.76
X-RAY DIFFRACTIONt_other_torsion16.68
LS refinement shellResolution: 1.4→1.41 Å
RfactorNum. reflection% reflection
Rfree0.3174 75 -
Rwork0.3209 --
obs0.3207 1429 97.3 %
Refinement TLS params.Origin x: 15.1002 Å / Origin y: -14.3815 Å / Origin z: -12.557 Å
111213212223313233
T0.1813 Å2-0.004 Å20.0111 Å2-0.1417 Å2-0.002 Å2--0.1338 Å2
L1.0694 °2-0.0299 °20.6787 °2-0.7629 °2-0.2582 °2--2.2775 °2
S0.0405 Å °-0.1343 Å °0.1371 Å °-0.1343 Å °0.0343 Å °0.0557 Å °0.1371 Å °0.0557 Å °-0.0747 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A28 - 309
2X-RAY DIFFRACTION1{ *|* }A401
3X-RAY DIFFRACTION1{ *|* }B1 - 2
4X-RAY DIFFRACTION1{ *|* }C1 - 293
5X-RAY DIFFRACTION1{ *|* }M24 - 29
6X-RAY DIFFRACTION1{ *|* }W1 - 14

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