Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.29 kDa 
• Atom Count: 3046 
• Modelled Residue Count: 324 
• Deposited Residue Count: 331 
• Unique protein chains: 1

2ATM

Crystal structure of the recombinant allergen Ves v 2

• PDB DOI: 10.2210/pdb2ATM/pdb

• Classification: HYDROLASE
• Organism(s): Vespula vulgaris
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-08-25 Released: 2006-05-23 
• Deposition Author(s): Skov, L.K., Seppala, U., Coen, J.J.F., Crickmore, N., King, T.P., Monsalve, R., Kastrup, J.S., Spangfort, M.D., Gajhede, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structure of recombinant Ves v 2 at 2.0 Angstrom resolution: structural analysis of an allergenic hyaluronidase from wasp venom.

Skov, L.K., Seppala, U., Coen, J.J., Crickmore, N., King, T.P., Monsalve, R., Kastrup, J.S., Spangfort, M.D., Gajhede, M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 595-604

• PubMed: 16699186 
• DOI: 10.1107/S0907444906010687
• Primary Citation of Related Structures:  
  2ATM


• PubMed Abstract: 
  

Wasp venom from Vespula vulgaris contains three major allergens: Ves v 1, Ves v 2 and Ves v 5. Here, the cloning, expression, biochemical characterization and crystal structure determination of the hyaluronidase Ves v 2 from family 56 of the glycoside hydrolases are reported. The allergen was expressed in Escherichia coli as an insoluble protein and refolded and purified to obtain full enzymatic activity. Three N-glycosylation sites at Asn79, Asn99 and Asn127 were identified in Ves v 2 from a natural source by enzymatic digestions combined with MALDI-TOF mass spectrometry. The crystal structure of recombinant Ves v 2 was determined at 2.0 A resolution and reveals a central (beta/alpha)(7) core that is further stabilized by two disulfide bonds (Cys19-Cys308 and Cys185-Cys197). Based on sequence alignments and structural comparison with the honeybee allergen Api m 2, it is proposed that a conserved cavity near the active site is involved in binding of the substrate. Surface epitopes and putative glycosylation sites have been compared with those of two other major group 2 allergens from Apis mellifera (honeybee) and Dolichovespula maculata (white-faced hornet). The analysis suggests that the harboured allergic IgE-mediated cross-reactivity between Ves v 2 and the allergen from D. maculata is much higher than that between Ves v 2 and the allergen from A. mellifera.

---

Organizational Affiliation: 

Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronoglucosaminidase	A	331	Vespula vulgaris	Mutation(s): 1  EC: 3.2.1.35
UniProt
Find proteins for P49370 (Vespula vulgaris) Explore P49370  Go to UniProtKB:  P49370

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SME	A	L-PEPTIDE LINKING	C5 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.674	α = 90
b = 95.056	β = 90
c = 100.326	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-25 
• Released Date: 2006-05-23 
Deposition Author(s): Skov, L.K., Seppala, U., Coen, J.J.F., Crickmore, N., King, T.P., Monsalve, R., Kastrup, J.S., Spangfort, M.D., Gajhede, M.

Revision History  

• Version 1.0: 2006-05-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description