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- PDB-1h2o: SOLUTION STRUCTURE OF THE MAJOR CHERRY ALLERGEN PRU AV 1 MUTANT E45W -

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Basic information

Entry
Database: PDB / ID: 1h2o
TitleSOLUTION STRUCTURE OF THE MAJOR CHERRY ALLERGEN PRU AV 1 MUTANT E45W
ComponentsMAJOR ALLERGEN PRU AV 1
KeywordsALLERGEN / MAJOR CHERRY ALLERGEN / PATHOGENESIS-RELATED PROTEIN / HETERONUCLEAR NMR / PLANT DEFENSE
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major allergen Pru av 1
Similarity search - Component
Biological speciesPRUNUS AVIUM (sweet cherry)
MethodSOLUTION NMR / simulated annealing
AuthorsNeudecker, P. / Lehmann, K. / Nerkamp, J. / Schweimer, K. / Sticht, H. / Boehm, M. / Scheurer, S. / Vieths, S. / Roesch, P.
Citation
Journal: Biochem.J. / Year: 2003
Title: Mutational Epitope Analysis of Pru Av 1 and Api G 1, the Major Allergens of Cherry (Prunus Avium) and Celery (Apium Graveolens): Correlating Ige Reactivity with Three-Dimensional Structure
Authors: Neudecker, P. / Lehmann, K. / Nerkamp, J. / Haase, T. / Wangorsch, A. / Fotisch, K. / Hoffmann, S. / Roesch, P. / Vieths, S. / Scheurer, S.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Allergic Cross-Reactivity Made Visible: Solution Structure of the Major Cherry Allergen Pru Av 1
Authors: Neudecker, P. / Schweimer, K. / Nerkamp, J. / Scheurer, S. / Vieths, S. / Sticht, H. / Roesch, P.
#2: Journal: J.Biomol.NMR / Year: 2001
Title: Improving the Efficiency of the Gaussian Conformational Database Potential for the Refinement of Protein and Nucleic Acid Structures
Authors: Neudecker, P. / Sticht, H. / Roesch, P.
#3: Journal: J.Biomol.NMR / Year: 2000
Title: Sequence-Specific 1H, 13C and 15N Resonance Assignments of the Major Cherry Allergen Pru a 1
Authors: Neudecker, P. / Schweimer, K. / Nerkamp, J. / Boehm, M. / Scheurer, S. / Vieths, S. / Sticht, H. / Roesch, P.
#4: Journal: Appl.Magn.Reson. / Year: 1999
Title: NMR Spectroscopy Reveals Common Structural Features of the Birch Pollen Allergen Bet V 1 and the Cherry Allergen Pru a 1
Authors: Schweimer, K. / Sticht, H. / Nerkamp, J. / Boehm, M. / Breitenbach, M. / Vieths, S. / Roesch, P.
History
DepositionAug 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR ALLERGEN PRU AV 1


Theoretical massNumber of molelcules
Total (without water)17,6111
Polymers17,6111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 60LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein MAJOR ALLERGEN PRU AV 1 / PRU A 1


Mass: 17610.775 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION GLU 45 TRP / Source: (gene. exp.) PRUNUS AVIUM (sweet cherry) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O24248
Compound detailsPLANT DEFENSE PROTEIN, MEMBER OF THE BETV1 FAMILY OF PATHOGENESIS-RELATED PROTEINS. ENGINEERED ...PLANT DEFENSE PROTEIN, MEMBER OF THE BETV1 FAMILY OF PATHOGENESIS-RELATED PROTEINS. ENGINEERED MUTATION GLU 46 TRP

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
1211H
13115N-HSQC
141HNHA
1513D-1H
16115N-TOCSY-HSQC
1713D-1H
18115N-NOESY-HSQC
1913D-1H
110115N/1H
111115N-HMQC-NOESY-HSQC
NMR detailsText: THE CHANGES IN STRUCTURE COMPARED TO PRU AV 1 WT WERE DETERMINED USING DOUBLE-RESONANCE NMR SPECTROSCOPY ON 15N-LABELED PRU AV 1 E45W

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Sample preparation

DetailsContents: 90% H2O / 10% D2O
Sample conditionsIonic strength: 50 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH1.2.1BRUNGER, CLORE, KUSZEWSKI, SCHWIETERS, TJrefinement
NDEEstructure solution
NMRView5.0.4structure solution
Xplor-NIH1.2.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 60 / Conformers submitted total number: 24

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