3LEG | pdb_00003leg

Lectin Domain of Lectinolysin complexed with Lewis Y Antigen

• PDB DOI: https://doi.org/10.2210/pdb3LEG/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Streptococcus mitis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-14 Released: 2010-12-29 
• Deposition Author(s): Feil, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.234 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure of the lectin regulatory domain of the cholesterol-dependent cytolysin lectinolysin reveals the basis for its lewis antigen specificity.

Feil, S.C., Lawrence, S., Mulhern, T.D., Holien, J.K., Hotze, E.M., Farrand, S., Tweten, R.K., Parker, M.W.

(2012) Structure 20: 248-258

• PubMed: 22325774 
• DOI: https://doi.org/10.1016/j.str.2011.11.017
• Primary Citation Related Structures: 
  3LE0, 3LEG, 3LEI, 3LEK


• PubMed Abstract: 
  

  The cholesterol-dependent cytolysins (CDCs) punch holes in target cell membranes through a highly regulated process. Streptococcus mitis lectinolysin (LLY) exhibits another layer of regulation with a lectin domain that enhances the pore-forming activity of the toxin. We have determined the crystal structures of the lectin domain by itself and in complex with various glycans that reveal the molecular basis for the Lewis antigen specificity of LLY. A small-angle X-ray scattering study of intact LLY reveals the molecule is flat and elongated with the lectin domain oriented so that the Lewis antigen-binding site is exposed. We suggest that the lectin domain enhances the pore-forming activity of LLY by concentrating toxin molecules at fucose-rich sites on membranes, thus promoting the formation of prepore oligomers on the surface of susceptible cells.

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Organizational Affiliation: 
• Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, 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: 17.64 kDa 
• Atom Count: 1,284 
• Modeled Residue Count: 142 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet aggregation factor Sm-hPAF	A	153	Streptococcus mitis	Mutation(s): 1  Gene Names: samhpaf
UniProt
Find proteins for Q2PHL4 (Streptococcus mitis) Explore Q2PHL4  Go to UniProtKB:  Q2PHL4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan: G00052MO GlyCosmos: G00052MO GlyGen: G00052MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900054	B	Lewis Y antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.234 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.06	α = 90
b = 67.06	β = 90
c = 98.67	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Feil, S.C.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-13
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description