4YHD

Staphylococcal alpha-hemolysin H35A mutant monomer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for pore-forming mechanism of staphylococcal alpha-hemolysin

Sugawara, T.Yamashita, D.Kato, K.Peng, Z.Ueda, J.Kaneko, J.Kamio, Y.Tanaka, Y.Yao, M.

(2015) Toxicon 108: 226-231

  • DOI: 10.1016/j.toxicon.2015.09.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Staphylococcal α-hemolysin (α-HL) is a β-barrel pore-forming toxin (PFT) expressed by Staphylococcus aureus. α-HL is secreted as a water-soluble monomeric protein, which binds to target membranes and forms membrane-inserted heptameric pores. To explo ...

    Staphylococcal α-hemolysin (α-HL) is a β-barrel pore-forming toxin (PFT) expressed by Staphylococcus aureus. α-HL is secreted as a water-soluble monomeric protein, which binds to target membranes and forms membrane-inserted heptameric pores. To explore the pore-forming mechanism of α-HL in detail, we determined the crystal structure of the α-HL monomer and prepore using H35A mutant and W179A/R200A mutant, respectively. Although the overall structure of the monomer was similar to that of other staphylococcal PFTs, a marked difference was observed in the N-terminal amino latch, which bent toward the prestem. Moreover, the prestem was fastened by the cap domain with a key hydrogen bond between Asp45 and Tyr118. Prepore structure showed that the transmembrane region is roughly formed with flexibility, although the upper half of the β-barrel is formed appropriately. Structure comparison among monomer, prepore and pore revealed a series of motions, in which the N-terminal amino latch released upon oligomerization destroys its own key hydrogen bond between Asp45-Tyr118. This action initiated the protrusion of the prestem. Y118F mutant and the N-terminal truncated mutant markedly decreased in the hemolytic activity, indicating the importance of the key hydrogen bond and the N-terminal amino latch on the pore formation. Based on these observations, we proposed a dynamic molecular mechanism of pore formation for α-HL.


    Organizational Affiliation

    Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-hemolysin
A, B, C, D, E, G
302Staphylococcus aureusMutation(s): 2 
Gene Names: hly (hla)
Find proteins for P09616 (Staphylococcus aureus)
Go to UniProtKB:  P09616
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, D, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.930α = 90.00
b = 128.910β = 91.57
c = 135.280γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan26102501

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2018-03-21
    Type: Data collection, Database references, Derived calculations