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- PDB-2nar: Solution structure of AVR3a_60-147 from Phytophthora infestans -

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Basic information

Entry
Database: PDB / ID: 2nar
TitleSolution structure of AVR3a_60-147 from Phytophthora infestans
ComponentsEffector protein Avr3a
KeywordsPROTEIN BINDING
Function / homologyRXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / : / host cell endosome / extracellular region / RxLR effector protein Avr3a
Function and homology information
Biological speciesPhytophthora infestans (potato late blight agent)
MethodSOLUTION NMR / simulated annealing, energy minimization
Model detailslowest energy, model1
AuthorsMatena, A. / Bayer, P. / Zhukov, I. / Stanek, J. / Kozminski, W. / van West, P. / Wawra, S.
CitationJournal: Plant Cell / Year: 2017
Title: The RxLR Motif of the Host Targeting Effector AVR3a ofPhytophthora infestansIs Cleaved before Secretion.
Authors: Wawra, S. / Trusch, F. / Matena, A. / Apostolakis, K. / Linne, U. / Zhukov, I. / Stanek, J. / Kozminski, W. / Davidson, I. / Secombes, C.J. / Bayer, P. / van West, P.
History
DepositionJan 8, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: Effector protein Avr3a


Theoretical massNumber of molelcules
Total (without water)11,5111
Polymers11,5111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Effector protein Avr3a / Effector protein Avr3a_KI


Mass: 11511.082 Da / Num. of mol.: 1 / Mutation: N7S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans (potato late blight agent)
Gene: Avr3a, PI35.0050, PI49.0530, putative / Production host: Escherichia coli (E. coli) / References: UniProt: E2DWQ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H COSY
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D (H)CCH-COSY
1613D (H)CCH-TOCSY
1713D HBHANH
1813D HBHA(CO)NH
19113C-NOESY-HSQC
110115N-NOESY-HSQC
11113D HNCO
11214D HN(CO)CA
11314D HN(CA)CO
11414D HBHACBCANH

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Sample preparation

DetailsContents: 50 mM Potassium phosphate, 10 % D2O, 90 % H2O, 50 uM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMPotassium phosphate-11
10 %D2O-21
90 %H2O-31
50 uMDSS-41
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7001
Varian VNMRSVarianVNMRS7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
YasaraKRIEGER E.refinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 61 / Protein psi angle constraints total count: 61
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.43 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 3.14 ° / Maximum upper distance constraint violation: 0.34 Å
NMR ensemble rmsDistance rms dev: 0.006 Å / Distance rms dev error: 0.0013 Å

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