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- PDB-6ne8: Solution Structure of the Thioredoxin-like Domain of Arabidopsis ... -

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Entry
Database: PDB / ID: 6ne8
TitleSolution Structure of the Thioredoxin-like Domain of Arabidopsis NCP (NUCLEAR CONTROL OF PEP ACTIVITY)
ComponentsThioredoxin-like fold domain-containing protein MRL7L, chloroplastic
KeywordsPLANT PROTEIN / NCP / NUCLEAR CONTROL OF PEP ACTIVITY / thioredoxin-like domain / chloroplast biogenesis / phytochrome signaling / plastid-encoded RNA polymerase
Function / homologychloroplast organization / chloroplast stroma / Thioredoxin-like superfamily / regulation of DNA-templated transcription / nucleus / Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiu, J. / Chen, M. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087388 United States
CitationJournal: Nat Commun / Year: 2019
Title: NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches.
Authors: Yang, E.J. / Yoo, C.Y. / Liu, J. / Wang, H. / Cao, J. / Li, F.W. / Pryer, K.M. / Sun, T.P. / Weigel, D. / Zhou, P. / Chen, M.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Assembly

Deposited unit
A: Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic


Theoretical massNumber of molelcules
Total (without water)16,6051
Polymers16,6051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic / Protein MESOPHYLL-CELL RNAI LIBRARY LINE 7-LIKE / AtMRL7-L / Protein SUPPRESSOR OF VARIEGATION 4-LIKE


Mass: 16605.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MRL7L, SVR4L, At2g31840 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SKB6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic2Triple-resonance
121isotropic24D (H)CCH-TOCSY
131isotropic24D H(CCO)NH
143isotropic13D 1H-15N NOESY
151isotropic14D 13C-HMQC-NOESY-15N-HSQC
162isotropic14D 13C-HMQC-NOESY-13C-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM [U-99% 13C; U-99% 15N] NCP (NUCLEAR CONTROL OF PEP ACTIVITY) Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 90% H2O/10% D2O15N/13C Sample H2O90% H2O/10% D2O
solution31.2 mM [U-99% 15N] NCP (NUCLEAR CONTROL OF PEP ACTIVITY) Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 90% H2O/10% D2O15N Sample H2O90% H2O/10% D2O
solution21.2 mM [U-99% 13C; U-99% 15N] NCP (NUCLEAR CONTROL OF PEP ACTIVITY) Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 100% D2O15N/13C Sample D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMNCP (NUCLEAR CONTROL OF PEP ACTIVITY) Thioredoxin-like Domain[U-99% 13C; U-99% 15N]1
1.2 mMNCP (NUCLEAR CONTROL OF PEP ACTIVITY) Thioredoxin-like Domain[U-99% 15N]3
1.2 mMNCP (NUCLEAR CONTROL OF PEP ACTIVITY) Thioredoxin-like Domain[U-99% 13C; U-99% 15N]2
25 mMHEPESnatural abundance1
25 mMHEPESnatural abundance2
25 mMHEPESnatural abundance3
50 mMKClnatural abundance1
50 mMKClnatural abundance2
50 mMKClnatural abundance3
10 mMDTTnatural abundance1
10 mMDTTnatural abundance2
10 mMDTTnatural abundance3
Sample conditionsDetails: ~1.2 mM protein in a buffer containing 25 mM HEPES, 50 mM KCl (pH 7.0), and 10 mM DTT.
Ionic strength: 50 mM / Label: NMR / pH: 7 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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