Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 51.96 kDa 
• Atom Count: 3909 
• Modelled Residue Count: 459 
• Deposited Residue Count: 463 
• Unique protein chains: 1

2XZ3

BLV TM hairpin

• PDB DOI: 10.2210/pdb2XZ3/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli, Bovine leukemia virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-22 Released: 2011-03-02 
• Deposition Author(s): Schuettelkopf, A.W., Lamb, D., Brighty, D.W., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Charge-Surrounded Pockets and Electrostatic Interactions with Small Ions Modulate the Activity of Retroviral Fusion Proteins.

Lamb, D., Schuttelkopf, A.W., Van Aalten, D.M.F., Brighty, D.W.

(2011) PLoS Pathog 7: 1268

• PubMed: 21304939 
• DOI: 10.1371/journal.ppat.1001268
• Primary Citation of Related Structures:  
  2XZ3


• PubMed Abstract: 
  

Refolding of viral class-1 membrane fusion proteins from a native state to a trimer-of-hairpins structure promotes entry of viruses into cells. Here we present the structure of the bovine leukaemia virus transmembrane glycoprotein (TM) and identify a group of asparagine residues at the membrane-distal end of the trimer-of-hairpins that is strikingly conserved among divergent viruses. These asparagines are not essential for surface display of pre-fusogenic envelope. Instead, substitution of these residues dramatically disrupts membrane fusion. Our data indicate that, through electrostatic interactions with a chloride ion, the asparagine residues promote assembly and profoundly stabilize the fusion-active structures that are required for viral envelope-mediated membrane fusion. Moreover, the BLV TM structure also reveals a charge-surrounded hydrophobic pocket on the central coiled coil and interactions with basic residues that cluster around this pocket are critical to membrane fusion and form a target for peptide inhibitors of envelope function. Charge-surrounded pockets and electrostatic interactions with small ions are common among class-1 fusion proteins, suggesting that small molecules that specifically target such motifs should prevent assembly of the trimer-of-hairpins and be of value as therapeutic inhibitors of viral entry.

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Organizational Affiliation: 

The Biomedical Research Institute, College of Medicine, Ninewells Hospital, The University of Dundee, Dundee, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MALTOSE ABC TRANSPORTER PERIPLASMIC PROTEIN, ENVELOPE GLYCOPROTEIN	A	463	Escherichia coli, Bovine leukemia virus This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q90M13 (Bovine leukemia virus) Explore Q90M13  Go to UniProtKB:  Q90M13
UniProt Groups	P0AEX9Q90M13

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.595	α = 90
b = 107.595	β = 90
c = 119.17	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-22 
• Released Date: 2011-03-02 
Deposition Author(s): Schuettelkopf, A.W., Lamb, D., Brighty, D.W., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references, Version format compliance
• Version 1.2: 2014-03-12
  Changes: Source and taxonomy
• Version 1.3: 2017-03-15
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary