4ZGH | pdb_00004zgh

Structure of Sugar Binding Protein Pneumolysin

• PDB DOI: https://doi.org/10.2210/pdb4ZGH/pdb

• Classification: Sugar binding protein, toxin
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2015-04-23 Released: 2016-03-09 
• Deposition Author(s): Parker, M.W., Feil, S.C., Morton, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.307 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation.

Lawrence, S.L., Feil, S.C., Morton, C.J., Farrand, A.J., Mulhern, T.D., Gorman, M.A., Wade, K.R., Tweten, R.K., Parker, M.W.

(2015) Sci Rep 5: 14352-14352

• PubMed: 26403197 
• DOI: https://doi.org/10.1038/srep14352
• Primary Citation Related Structures: 
  4ZGH


• PubMed Abstract: 
  

  Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world's leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface.

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Organizational Affiliation: 
• ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.69 kDa 
• Atom Count: 3,812 
• Modeled Residue Count: 473 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pneumolysin	A	477	Streptococcus pneumoniae D39	Mutation(s): 3  Gene Names: ply, SPD_1726 Membrane Entity: Yes
UniProt
Find proteins for Q04IN8 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04IN8  Go to UniProtKB:  Q04IN8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AUC	I [auth A], J [auth A]	GOLD (I) CYANIDE ION C2 Au N2 DGOHFTDNMSZWDQ-UHFFFAOYSA-N
PEG	G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.307 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.857	α = 90
b = 133.619	β = 90
c = 220.442	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Parker, M.W., Feil, S.C., Morton, C.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Advisory, Data collection, Derived calculations, Refinement description
• Version 1.2: 2019-02-13
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description