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- EMDB-48848: Cryo EM structure of LukAB (LukGH) toxin from Staphylococcus aure... -

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Basic information

Entry
Database: EMDB / ID: EMD-48848
TitleCryo EM structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
Map dataStructure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
Sample
  • Complex: LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
    • Protein or peptide: leukocidin-like protein 1
    • Protein or peptide: leukocidin-like protein 2
    • Protein or peptide: STAU-15 Heavy Chain
    • Protein or peptide: STAU-15 Light Chain
KeywordsmAb / TOXIN / IMMUNE SYSTEM-Toxin complex
Function / homologyBi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / cytolysis in another organism / extracellular region / Uncharacterized leukocidin-like protein 2 / Uncharacterized leukocidin-like protein 1
Function and homology information
Biological speciesStaphylococcus aureus (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI139172 United States
CitationJournal: To Be Published
Title: Cryo EM structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
Authors: Binshtein E / Crowe JE
History
DepositionJan 30, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48848.png

Downloads & links

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Map

FileDownload / File: emd_48848.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 359.92 Å		1.12 Å/pix.
x 320 pix.
= 359.92 Å		1.12 Å/pix.
x 320 pix.
= 359.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12475 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017840378 - 2.146112
Average (Standard dev.)0.00036706813 (±0.014236644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 359.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_48848_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48848_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LukAB (LukGH) toxin from Staphylococcus aureus in complex with ne...

EntireName: LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
Components
  • Complex: LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
    • Protein or peptide: leukocidin-like protein 1
    • Protein or peptide: leukocidin-like protein 2
    • Protein or peptide: STAU-15 Heavy Chain
    • Protein or peptide: STAU-15 Light Chain

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Supramolecule #1: LukAB (LukGH) toxin from Staphylococcus aureus in complex with ne...

SupramoleculeName: LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: leukocidin-like protein 1

MacromoleculeName: leukocidin-like protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 35.825539 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SLKINSEIKQ VSEKNLDGDT KMYTRTATTS DSQKNITQSL QFNFLTEPNY DKETVFIKAK GTIGSGLRIL DPNGYWNSTL RWPGSYSVS IQNVDDNNNT NVTDFAPKNQ DESREVKYTY GYKTGGDFSI NRGGLTGNIT KESNYSETIS YQQPSYRTLL D QSTSHKGV ...String:
SLKINSEIKQ VSEKNLDGDT KMYTRTATTS DSQKNITQSL QFNFLTEPNY DKETVFIKAK GTIGSGLRIL DPNGYWNSTL RWPGSYSVS IQNVDDNNNT NVTDFAPKNQ DESREVKYTY GYKTGGDFSI NRGGLTGNIT KESNYSETIS YQQPSYRTLL D QSTSHKGV GWKVEAHLIN NMGHDHTRQL TNDSDNRTKS EIFSLTRNGN LWAKDNFTPK DKMPVTVSEG FNPEFLAVMS HD KKDKGKS QFVVHYKRSM DEFKIDWNRH GFWGYWSGEN HVDKKEEKLS ALYEVDWKTH NVKFVKVLND NEKK

UniProtKB: Uncharacterized leukocidin-like protein 1

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Macromolecule #2: leukocidin-like protein 2

MacromoleculeName: leukocidin-like protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 37.143102 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: DSQDQNKKEH VDKSQQKDKR NVTNKDKNST APDDIGKNGK ITKRTETVYD EKTNILQNLQ FDFIDDPTYD KNVLLVKKQG SIHSNLKFE SHKEEKNSNW LKYPSEYHVD FQVKRNRKTE ILDQLPKNKI STAKVDSTFS YSSGGKFDST KGIGRTSSNS Y SKTISYNQ ...String:
DSQDQNKKEH VDKSQQKDKR NVTNKDKNST APDDIGKNGK ITKRTETVYD EKTNILQNLQ FDFIDDPTYD KNVLLVKKQG SIHSNLKFE SHKEEKNSNW LKYPSEYHVD FQVKRNRKTE ILDQLPKNKI STAKVDSTFS YSSGGKFDST KGIGRTSSNS Y SKTISYNQ QNYDTIASGK NNNWHVHWSV IANDLKYGGE VKNRNDELLF YRNTRIATVE NPELSFASKY RYPALVRSGF NP EFLTYLS NEKSNEKTQF EVTYTRNQDI LKNRPGIHYA PPILEKNKDG QRLIVTYEVD WKNKTVKVVD KYSDDNKPYK EG

UniProtKB: Uncharacterized leukocidin-like protein 2

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Macromolecule #3: STAU-15 Heavy Chain

MacromoleculeName: STAU-15 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.288911 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGGG VVQPGRSLRL SCAASGFSFS TYDMNWVRQA PGKGLEWLSI ISYDETNKYY ADSVKGRFTI SRDNSKNTLF LQMNSLKPE DSAVYHCVKV GWTLVGDGVD MWGQGTLVTV SS

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Macromolecule #4: STAU-15 Light Chain

MacromoleculeName: STAU-15 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.438823 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIRMTQSPSS LSASVGDRVT ISCRASQGIS HYLAWYQQQP GKVPKLLIYA ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNGAPFTFG PGTKVDIK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 24959 / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121805
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9n38:
Cryo EM structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15

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