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- PDB-6alk: NMR solution structure of the major beech pollen allergen Fag s 1 -

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Basic information

Entry
Database: PDB / ID: 6alk
TitleNMR solution structure of the major beech pollen allergen Fag s 1
ComponentsFag s 1 pollen allergen
KeywordsALLERGEN / ligand binding / conformational diversity
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
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
Fag s 1 pollen allergen
Similarity search - Component
Biological speciesFagus sylvatica (European beech)
MethodSOLUTION NMR / simulated annealing
AuthorsMoraes, A.H. / Asam, A. / Almeida, F.C.L. / Wallner, M. / Ferreira, F. / Valente, A.P.
Funding support Brazil, 3items
OrganizationGrant numberCountry
FAPERJ202.902/2015 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303785/2014-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)426265/2016-5 Brazil
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis for cross-reactivity and conformation fluctuation of the major beech pollen allergen Fag s 1.
Authors: Moraes, A.H. / Asam, C. / Almeida, F.C.L. / Wallner, M. / Ferreira, F. / Valente, A.P.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 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:
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Assembly

Deposited unit
A: Fag s 1 pollen allergen


Theoretical massNumber of molelcules
Total (without water)17,2501
Polymers17,2501
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fag s 1 pollen allergen


Mass: 17250.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fagus sylvatica (European beech) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Star / References: UniProt: B7TWE6

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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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic33D CBCA(CO)NH
151isotropic33D HN(CA)CB
171isotropic33D HNCA
161isotropic33D HNCO
1101isotropic23D HBHA(CO)NH
191isotropic23D HN(CO)CA
181isotropic23D (H)CCH-TOCSY
1121isotropic23D 1H-15N NOESY
1111isotropic23D (H)CCH-COSY
1141isotropic23D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 600 uM [U-99% 13C; U-99% 15N] Fag s 1, 10 mM sodium phosphate, 150 mM sodium chloride, 5 % [U-100% 2H] TFE, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O
Details: 600 micromolar of isotopically labeled (15N, 13C) Fag s 1 in 10 mM of sodium phosphate, 150 mM NaCl pH 7.8 containing 5 % of deuterated 2,2,2 trifluoroethanol-D2 (TFE) and 10 % of D2O.
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMFag s 1[U-99% 13C; U-99% 15N]1
10 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
5 %TFE[U-100% 2H]1
10 %D2O[U-100% 2H]1
Sample conditionsDetails: 600 micromolar of isotopically labeled (15N, 13C) Fag s 1 in 10 mM of sodium phosphate, 150 mM NaCl pH 7.8 containing 5 % of deuterated 2,2,2 trifluoroethanol-D2 (TFE) and 10 % of D2O. The ...Details: 600 micromolar of isotopically labeled (15N, 13C) Fag s 1 in 10 mM of sodium phosphate, 150 mM NaCl pH 7.8 containing 5 % of deuterated 2,2,2 trifluoroethanol-D2 (TFE) and 10 % of D2O. The experiments were acquired at 308 K.
Ionic strength: 0.187 M / Label: condition 1 / pH: 7.8 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 308 K / Temperature err: 1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameVersionDeveloperClassification
Analysis2.4.1CcpNmr Analysis was primarily written by Wayne Boucher and Tim Stevens at the University of Cambridgechemical shift assignment
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure calculation
CNS1.3.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Analysis2.4.1CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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