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- PDB-7p93: Crystal Structure of leukotoxin LukE from Staphylococcus aureus i... -

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Basic information

Entry
Database: PDB / ID: 7p93
TitleCrystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide
Components
  • Atypical chemokine receptor 1
  • Leucotoxin LukEv
KeywordsTOXIN / leukotoxin / beta barrel pore forming toxin / cytolysis / hemolysis
Function / homology
Function and homology information


regulation of chemokine production / cytolysis in another organism / C-C chemokine binding / chemokine-mediated signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / defense response / recycling endosome / transmembrane signaling receptor activity / signaling receptor activity ...regulation of chemokine production / cytolysis in another organism / C-C chemokine binding / chemokine-mediated signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / defense response / recycling endosome / transmembrane signaling receptor activity / signaling receptor activity / toxin activity / early endosome / inflammatory response / extracellular region / plasma membrane
Similarity search - Function
Duffy antigen/chemokine receptor / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily
Similarity search - Domain/homology
Atypical chemokine receptor 1 / Leucotoxin LukEv
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
B: Atypical chemokine receptor 1
M: Atypical chemokine receptor 1


Theoretical massNumber of molelcules
Total (without water)37,6983
Polymers37,6983
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-1 kcal/mol
Surface area13730 Å2
Unit cell
Length a, b, c (Å)62.967, 71.181, 79.234
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 Atypical chemokine receptor 1 / Duffy antigen/chemokine receptor / Fy glycoprotein / GpFy / Glycoprotein D / Plasmodium vivax receptor


Mass: 1505.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16570
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
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: 1.55→47.16 Å / Num. obs: 51899 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.998 / Net I/σ(I): 17.5
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 2552 / CC1/2: 0.622

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8S

7p8s


Resolution: 1.55→47.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.071 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 2662 -RANDOM
Rwork0.1812 ---
obs0.1824 51740 98.8 %-
Displacement parametersBiso mean: 38.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.0761 Å20 Å20 Å2
2---6.8426 Å20 Å2
3---5.7665 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.55→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 215 2584
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.163375HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d859SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes436HARMONIC5
X-RAY DIFFRACTIONt_it2481HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion320SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2309SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.4
X-RAY DIFFRACTIONt_other_torsion15.09
LS refinement shellResolution: 1.55→1.56 Å
RfactorNum. reflection% reflection
Rfree0.3173 47 -
Rwork0.2714 --
obs0.2734 1035 99.17 %
Refinement TLS params.Origin x: 15.2077 Å / Origin y: -14.5851 Å / Origin z: -13.0666 Å
111213212223313233
T0.0061 Å2-0.008 Å20.0065 Å2--0.0455 Å2-0.0057 Å2---0.0374 Å2
L1.4266 °2-0.1156 °20.9883 °2-0.8604 °2-0.4985 °2--2.8297 °2
S0.0629 Å °-0.1708 Å °0.2242 Å °-0.1708 Å °0.0517 Å °0.111 Å °0.2242 Å °0.111 Å °-0.1146 Å °
Refinement TLS groupSelection details: { A|* }

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