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- PDB-6y3k: NMR solution structure of the hazelnut allergen Cor a 1.0403 -

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Basic information

Entry
Database: PDB / ID: 6y3k
TitleNMR solution structure of the hazelnut allergen Cor a 1.0403
ComponentsMajor allergen variant Cor a 1.0403
KeywordsALLERGEN / PR-10 protein / hazelnut allergen / Bet v 1 cross reactive protein
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START-like domain superfamily
Similarity search - Domain/homology
Major allergen variant Cor a 1.0403
Similarity search - Component
Biological speciesCorylus avellana (European hazelnut)
MethodSOLUTION NMR / simulated annealing
AuthorsFuehrer, S. / Kamenik, A.S. / Zeindl, R. / Nothegger, B. / Hofer, F. / Reider, N. / Liedl, K.R. / Tollinger, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP26849 Austria
Austrian Research Promotion Agency858017 Austria
CitationJournal: Sci Rep / Year: 2021
Title: Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens.
Authors: Fuhrer, S. / Kamenik, A.S. / Zeindl, R. / Nothegger, B. / Hofer, F. / Reider, N. / Liedl, K.R. / Tollinger, M.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major allergen variant Cor a 1.0403


Theoretical massNumber of molelcules
Total (without water)17,4211
Polymers17,4211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8640 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major allergen variant Cor a 1.0403


Mass: 17420.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corylus avellana (European hazelnut) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q9FPK3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-15N HSQC NH2 only
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-13C HSQC aromatic
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D HN(CA)CB
181isotropic13D CBCA(CO)NH
191isotropic13D (H)CCH-TOCSY
1102isotropic13D 1H-15N TOCSY
1111isotropic13D (H)CC(CO)NH-TOCSY
1122isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] Cor a 1.0403, 20 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O15N-13C-Cor a 1.040390% H2O/10% D2O
solution20.5 mM [U-99% 15N] Cor a 1.0403, 20 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O15N-Cor a 1.040390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCor a 1.0403[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
2 mMDTTnatural abundance1
0.5 mMCor a 1.0403[U-99% 15N]2
20 mMsodium phosphatenatural abundance2
2 mMDTTnatural abundance2
Sample conditionsIonic strength units: Not defined / Label: Conditions / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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