6ANY | pdb_00006any

Structure of BmVAL-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.214 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Crystal structure of Brugia malayi venom allergen-like protein-1 (BmVAL-1), a vaccine candidate for lymphatic filariasis.

Darwiche, R.Lugo, F.Drurey, C.Varossieau, K.Smant, G.Wilbers, R.H.P.Maizels, R.M.Schneiter, R.Asojo, O.A.

(2018) Int J Parasitol 48: 371-378

  • DOI: https://doi.org/10.1016/j.ijpara.2017.12.003
  • Primary Citation Related Structures: 
    6ANY

  • PubMed Abstract: 

    Brugia malayi is a causative agent of lymphatic filariasis, a major tropical disease. The infective L3 parasite stage releases immunomodulatory proteins including the venom allergen-like proteins (VALs), which are members of the SCP/TAPS (Sperm-coating protein/Tpx/antigen 5/pathogenesis related-1/Sc7) superfamily. BmVAL-1 is a major target of host immunity with >90% of infected B. malayi microfilaraemic cases being seropositive for antibodies to BmVAL-1. This study is part of ongoing efforts to characterize the structures and functions of important B. malayi proteins. Recombinant BmVAL-1 was produced using a plant expression system, crystallized and the structure was solved by molecular replacement and refined to 2.1 Å, revealing the characteristic alpha/beta/alpha sandwich topology of eukaryotic SCP/TAPS proteins. The protein has more than 45% loop regions and these flexible loops connect the helices and strands, which are longer than predicted based on other parasite SCP/TAPS protein structures. The large central cavity of BmVAL-1 is a prototypical CRISP cavity with two histidines required to bind divalent cations. The caveolin-binding motif (CBM) that mediates sterol binding in SCP/TAPS proteins is large and open in BmVAL-1 and is N-glycosylated. N-glycosylation of the CBM does not affect the ability of BmVAL-1 to bind sterol in vitro. BmVAL-1 complements the in vivo sterol export phenotype of yeast mutants lacking their endogenous SCP/TAPS proteins. The in vitro sterol-binding affinity of BmVAL-1 is comparable with Pry1, a yeast sterol transporting SCP/TAPS protein. Sterol binding of BmVAL-1 is dependent on divalent cations. BmVAL-1 also has a large open palmitate-binding cavity, which binds palmitate comparably to tablysin-15, a lipid-binding SCP/TAPS protein. The central cavity, CBM and palmitate-binding cavity of BmVAL-1 are interconnected within the monomer with channels that can serve as pathways for water molecules, cations and small molecules.


  • Organizational Affiliation
    • Division of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, CH 1700 Fribourg, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 24.53 kDa 
  • Atom Count: 1,883 
  • Modeled Residue Count: 206 
  • Deposited Residue Count: 206 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bm4233, isoform b206Brugia malayiMutation(s): 0 
Gene Names: Bm4233BM_Bm4233
UniProt
Find proteins for A0A0J9Y762 (Brugia malayi)
Explore A0A0J9Y762 
Go to UniProtKB:  A0A0J9Y762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9Y762
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G80587NA
GlyCosmos: G80587NA
GlyGen: G80587NA
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G18638YB
GlyCosmos: G18638YB
GlyGen: G18638YB

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.214 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.79α = 90
b = 85.79β = 90
c = 66.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2018-03-28 
  • Deposition Author(s): Asojo, O.A.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary