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- PDB-6gq9: Solution structure of the hazel allergen Cor a 1.0401 -

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Basic information

Entry
Database: PDB / ID: 6gq9
TitleSolution structure of the hazel allergen Cor a 1.0401
ComponentsMajor allergen Cor a 1.0401
KeywordsALLERGEN / PR-10 allergen / hydrophobic pocket / Bet v 1 homologue
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
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 Cor a 1.0401
Similarity search - Component
Biological speciesCorylus avellana (European hazelnut)
MethodSOLUTION NMR / simulated annealing
AuthorsJacob, T.P. / Schweimer, K. / Seutter von Loetzen, C. / Woehrl, B.M.
CitationJournal: Sci Rep / Year: 2019
Title: Identification of a natural ligand of the hazel allergen Cor a 1.
Authors: Jacob, T. / von Loetzen, C.S. / Reuter, A. / Lacher, U. / Schiller, D. / Schobert, R. / Mahler, V. / Vieths, S. / Rosch, P. / Schweimer, K. / Wohrl, B.M.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major allergen Cor a 1.0401


Theoretical massNumber of molelcules
Total (without water)17,6061
Polymers17,6061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10770 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 240structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major allergen Cor a 1.0401


Mass: 17606.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corylus avellana (European hazelnut) / Gene: CORA1.0401 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SWR4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D HN(CO)CA
171isotropic13D HN(COCA)CB
181isotropic23D 1H-15N NOESY
191isotropic13D (H)NNH NOESY HSQC
1101isotropic23D 1H-13C NOESY
1111isotropic13D C(CO)NH
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D CCH-TOCSY
1141isotropic13D HBHA(CO)NH
1151isotropic13D (H)CCH-NOESY HSQC
1161isotropic12D 1H-13C HSQC aromatic
1171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-13C; U-15N] Cor a 1.0401, 2 mM DTT, 10 mM sodium phosphate, 90% H2O/10% D2O
Label: Cor a 1.0401 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCor a 1.0401[U-13C; U-15N]1
2 mMDTTnatural abundance1
10 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 10 mM sodium phosphate mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7001
Bruker AvanceBrukerAvance10002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 240 / Conformers submitted total number: 20

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