9M4P | pdb_00009m4p

Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9M4P

This is version 1.1 of the entry. See complete history

Literature

Stepwise assembly of alpha-hemolysin from intermediates to the mature pore in native erythrocytes.

Chatterjee, A.Roy, A.Das, P.P.Chakraborty, D.Ghoshal, B.Jhunjhunwala, S.Dutta, S.

(2026) J Cell Biol 225

  • DOI: https://doi.org/10.1083/jcb.202506129
  • Primary Citation Related Structures: 
    9M4A, 9M4P, 9MBX, 9UFA, 9VFW

  • PubMed Abstract: 

    Alpha-hemolysin (α-HL) is a small pore-forming toxin secreted by pathogenic Staphylococcus aureus, inducing cell death process by forming pores in membrane. So far, detergents or artificial lipid environments have been utilized to characterize the toxin structure. The toxin-induced changes in the membrane, membrane remodeling after toxin treatment, and the role of the toxin during pore formation process remain ambiguous. Thus, understanding pore formation in the cellular environment, including the roles of the plasma membrane and lipid composition, is crucial for drug development. In this study, we captured step-by-step oligomerization of α-HL and membrane rupture of erythrocyte cells using confocal microscopy, cryo-EM imaging, and single-particle analysis. We resolved 3.1-3.8 Å resolution structures of pore, prepore, and immature pore conformations in cellular environment. Furthermore, mass spectrometry analysis demonstrated key erythrocyte lipid components interacting with α-HL. Our findings indicate that shorter or unsaturated lipid chains facilitate pore formation and the role of phosphatidylcholine with varying physical properties in modulating the toxin's activity.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science , Bengaluru, India.

Macromolecule Content 

  • Total Structure Weight: 233.03 kDa 
  • Atom Count: 16,415 
  • Modeled Residue Count: 2,051 
  • Deposited Residue Count: 2,051 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-hemolysin293Staphylococcus aureusMutation(s): 0 
Gene Names: hlyhla
UniProt
Find proteins for P09616 (Staphylococcus aureus)
Explore P09616 
Go to UniProtKB:  P09616
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09616
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)India--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Data collection, Database references