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- PDB-2ncg: The CC domain structure from the wheat stem rust resistance prote... -

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Basic information

Entry
Database: PDB / ID: 2ncg
TitleThe CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins
ComponentsRGA1e
KeywordsUNKNOWN FUNCTION / coiled-coil domain
Function / homology
Function and homology information


ADP binding / defense response / ATP binding
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesAegilops tauschii (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model1
AuthorsLavrencic, P. / Mobli, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins.
Authors: Casey, L.W. / Lavrencic, P. / Bentham, A.R. / Cesari, S. / Ericsson, D.J. / Croll, T. / Turk, D. / Anderson, P.A. / Mark, A.E. / Dodds, P.N. / Mobli, M. / Kobe, B. / Williams, S.J.
History
DepositionMar 30, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Aug 24, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RGA1e


Theoretical massNumber of molelcules
Total (without water)13,1381
Polymers13,1381
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)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein RGA1e


Mass: 13138.331 Da / Num. of mol.: 1 / Fragment: Coiled-coil domain residues 6-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aegilops tauschii (plant) / Gene: Sr33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: S5DUP7, UniProt: S5DMB1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HCACO
1613D (H)CCH-COSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D HBHA(CO)NH

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Sample preparation

DetailsContents: 450 uM [U-100% 13C; U-100% 15N] protein, 10 mM HEPES, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMentity-1[U-100% 13C; U-100% 15N]1
10 mMHEPES-21
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TALOSTALOS+Cornilescu, Delaglio and Baxgeometry optimization
CCPNMR2.4.1Vranken WF et al.peak picking
CCPNMR2.4.1Vranken WF et al.data analysis
Rowland_NMR_toolkit3JC Hoch et al.processing
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: automated NOE assignment
NMR constraintsNOE constraints total: 1516 / NOE intraresidue total count: 580 / NOE long range total count: 259 / NOE medium range total count: 283 / NOE sequential total count: 394 / Protein phi angle constraints total count: 112 / Protein psi angle constraints total count: 112
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å

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