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7p93

Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide

Method: X-RAY DIFFRACTION Dmax: 82.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Leucotoxin LukEv

Staphylococcus aureus

UniProt Q2FXB0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 7–306 Not recorded Atypical chemokine receptor 1 × 2 （Q16570） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000 Resolution 1.55 Å R-free 0.204

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7P93 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3ROH Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL. Deposited 2011-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–306（306 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；Protein: 7mG/mL, 0.25M Sodium chloride, 0.01M Tris, pH 8.3. Screen: JCSG+, D7, 0.2M Lithium sulfate, 0.1M Tris, pH 8.5, 40% v/v PEG 400. VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.20 Å R-free 0.224
7P8S Crystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.9 Angstrom resolution Deposited 2021-07-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–306（300 aa）
Not recorded P6G HEXAETHYLENE GLYCOL × 1 MHA (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Ammonium sulfate, 0.05 M Magnesium sulfate heptahydrate, 0.1 M Sodium citrate pH 5.5 and 22.5 % v/v PEG Smear Medium
Resolution 1.90 Å R-free 0.203
7P8T Crystal Structure of leukotoxin LukE from Staphylococcus aureus at 1.5 Angstrom resolution Deposited 2021-07-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–306（300 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.46 Å R-free 0.194
7P8U Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with p-cresyl sulfate Deposited 2021-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–306（300 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 IMD IMIDAZOLE × 1 SO4 SULFATE ION × 1 6EI (4-methylphenyl) hydrogen sulfate × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.60 Å R-free 0.205
7P8X Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a doubly sulfated CCR2 N-terminal peptide Deposited 2021-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 7–306（300 aa）
Not recorded IMD IMIDAZOLE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.40 Å R-free 0.198

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUKEV_STAA8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–301； UniProt 7–306

Atypical chemokine receptor 1

OrganismNot specified

UniProt Q16570

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 34–46 Chain M； UniProt 34–46 Non-standard monomer：Yes (specific site not provided by mmCIF) Leucotoxin LukEv × 1 （Q2FXB0） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000 Resolution 1.55 Å R-free 0.204

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7P93 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NUU Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 14–43（30 aa） Fragment：unp residues 14-43
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 1.95 Å R-free 0.202
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 14–43（30 aa） Fragment：unp residues 14-43
Chain D 14–43（30 aa） Fragment：unp residues 14-43
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 2.60 Å R-free 0.233
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 14–43（30 aa） Fragment：unp residues 14-43
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 2.60 Å R-free 0.233
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 14–43（30 aa） Fragment：unp residues 14-43
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 2.60 Å R-free 0.233
8JPS Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map) Deposited 2023-06-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 46–312（267 aa）
Chain B 46–312（267 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å
8YNF Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8 Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–336（335 aa）
Chain B 2–336（335 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACKR1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–14； UniProt 34–46 Author chain M； PDBConstruct 2–14； UniProt 34–46

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7p93

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7p93
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7p93
Deposition date deposition_date2021-07-23
Structure title titleCrystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide
Keywords keywordsleukotoxin, beta barrel pore forming toxin, cytolysis, hemolysis, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.96 Å
Radius of gyration Rg (electron density) rg_electron22.27 Å
Forward intensity I(0) i019924100.00
Molecular weight molecular_weight33511.0 kDa
Excluded volume excluded_volume41718 ų
Envelope volume envelope_volume48910 ų
Hydration-shell volume shell_volume19454 ų
Envelope diameter envelope_diameter83.9 Å
Shell Rg shell_rg27.86 Å
Envelope Rg envelope_rg22.87 Å
Shape Rg shape_rg22.25 Å
Total Rg total_rg23.06 Å
Total atoms total_atoms2369
Residues n_residues296
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax82.0 Å
Rg (real space) rg_real23.15 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real1.9920e+07
I(0) uncertainty (real space) i0_real_error3.2270e+05
Rg (reciprocal space) rg_reciprocal23.11 Å
I(0) (reciprocal space) i0_reciprocal19920000.0000
Solution quality estimate total_estimate0.8146
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.7 Å
Skewness Skewness skewness0.582
Kurtosis Kurtosis kurtosis-0.158
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6783000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.625; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.736; Smooth: 0.982
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7p93A01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology240 — Leukocidin-like
Homologous superfamily homologous superfamily10 — Leukocidin/porin MspA
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8. Citations (1)

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9. Files and Curves (10)