9N38 | pdb_00009n38

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

PDB DOI: https://doi.org/10.2210/pdb9N38/pdb
EM Map EMD-48848: EMDB EMDataResource

Classification: IMMUNE SYSTEM/Toxin
Organism(s): Staphylococcus aureus, Homo sapiens
Expression System: Escherichia coli BL21, Homo sapiens
Mutation(s): No

Deposited: 2025-01-30 Released: 2026-02-04
Deposition Author(s): Binshtein, E., Crowe, J.E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9N38

This is version 1.0 of the entry. See complete history.

Literature

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

Binshtein, E., Crowe, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 97.7 kDa
Atom Count: 5,677
Modeled Residue Count: 703
Deposited Residue Count: 858
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
leukocidin-like protein 1	A	311	Staphylococcus aureus	Mutation(s): 0 Gene Names: SAUSA300_1974
UniProt
Find proteins for Q2FFA3 (Staphylococcus aureus (strain USA300)) Explore Q2FFA3 Go to UniProtKB: Q2FFA3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FFA3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
leukocidin-like protein 2	B	319	Staphylococcus aureus	Mutation(s): 0 Gene Names: SAUSA300_1975
UniProt
Find proteins for Q2FFA2 (Staphylococcus aureus (strain USA300)) Explore Q2FFA2 Go to UniProtKB: Q2FFA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FFA2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
STAU-15 Heavy Chain	C [auth H]	121	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
STAU-15 Light Chain	D [auth L]	107	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI139172

Revision History (Full details and data files)

Version 1.0: 2026-02-04
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.