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- PDB-8vu6: Wheat Germ Agglutinin (WGA) domain A -

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Basic information

Entry
Database: PDB / ID: 8vu6
TitleWheat Germ Agglutinin (WGA) domain A
ComponentsAgglutinin isolectin 1
KeywordsSUGAR BINDING PROTEIN / Lectin / Multidomain protein / Structural stability
Function / homology
Function and homology information


chitin binding / carbohydrate binding
Similarity search - Function
Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily
Similarity search - Domain/homology
Agglutinin isolectin 1
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodSOLUTION NMR / molecular dynamics
AuthorsTitaux-Delgado, G.A. / del Rio-Portilla, F. / Garcia-Hernandez, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN206221 Mexico
CitationJournal: Protein Sci. / Year: 2024
Title: Decoding the mechanism governing the structural stability of wheat germ agglutinin and its isolated domains: A combined calorimetric, NMR, and MD simulation study.
Authors: Medrano-Cerano, J.L. / Cofas-Vargas, L.F. / Leyva, E. / Rauda-Ceja, J.A. / Calderon-Vargas, M. / Cano-Sanchez, P. / Titaux-Delgado, G. / Melchor-Meneses, C.M. / Hernandez-Arana, A. / Del Rio- ...Authors: Medrano-Cerano, J.L. / Cofas-Vargas, L.F. / Leyva, E. / Rauda-Ceja, J.A. / Calderon-Vargas, M. / Cano-Sanchez, P. / Titaux-Delgado, G. / Melchor-Meneses, C.M. / Hernandez-Arana, A. / Del Rio-Portilla, F. / Garcia-Hernandez, E.
History
DepositionJan 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agglutinin isolectin 1


Theoretical massNumber of molelcules
Total (without water)4,7641
Polymers4,7641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Agglutinin isolectin 1 / Isolectin A / WGA1


Mass: 4764.283 Da / Num. of mol.: 1 / Fragment: Chitin-binding type-1 domain A, residues 26-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli (E. coli) / References: UniProt: P10968

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM WGA_domA, 95% H2O/5% D2O / Label: H1_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: WGA_domA / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.16 M / Label: 1 / pH: 4.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
XEASYBartels et al.peak picking
RefinementMethod: molecular dynamics / Software ordinal: 3 / Details: used also for simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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