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- PDB-7b7o: Solution structure of A. thaliana core TatA in DHPC micelles -

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Basic information

Entry
Database: PDB / ID: 7b7o
TitleSolution structure of A. thaliana core TatA in DHPC micelles
ComponentsSec-independent protein translocase protein TATA, chloroplastic
KeywordsMEMBRANE PROTEIN / twin-arginine translocase / micelles / bitopic membrane protein / amphiphilic helix
Function / homology
Function and homology information


protein transport within lipid bilayer / TAT protein transport complex / protein transport by the Tat complex / chloroplast envelope / chloroplast thylakoid membrane / protein homooligomerization / membrane
Similarity search - Function
Sec-independent protein translocase protein TatA/B/E / Sec-independent protein translocase protein TatA/E / mttA/Hcf106 family
Similarity search - Domain/homology
Sec-independent protein translocase protein TATA, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsPettersson, P. / Ye, W. / Jakob, M. / Tannert, F. / Klosgen, R.B. / Maler, L.
Funding support Sweden, Germany, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2014-3706 Sweden
German Research Foundation (DFG)KL 862/6-1 Germany
CitationJournal: FEBS J / Year: 2018
Title: Structure and dynamics of plant TatA in micelles and lipid bilayers studied by solution NMR.
Authors: Pettersson, P. / Ye, W. / Jakob, M. / Tannert, F. / Klosgen, R.B. / Maler, L.
History
DepositionDec 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: 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 1.2Jun 19, 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: Sec-independent protein translocase protein TATA, chloroplastic


Theoretical massNumber of molelcules
Total (without water)5,5361
Polymers5,5361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5580 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Sec-independent protein translocase protein TATA, chloroplastic / Protein THYLAKOID ASSEMBLY 4 / Protein TWIN-ARGININE TRANSLOCATION A


Mass: 5535.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TATA, THA4, At5g28750, T32B20.e / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LKU2

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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
131isotropic13D CBCANH
141isotropic13D CBCA(CO)NH
181isotropic13D HNCO
191isotropic13D HN(CA)CO
1101isotropic13D 1H-15N NOESY
1171isotropic13D 1H-13C NOESY
1111isotropic13D 1H-15N TOCSY
1161isotropic43D 1H-15N TOCSY
1121isotropic13D H(CCO)NH
1131isotropic13D C(CO)NH
1141isotropic13D (H)CCH-TOCSY
1152isotropic33D HNHA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle1200 uM [U-13C; U-15N] core AthTatA, 120 mM NA DHPC-d22, 20 mM NA sodium phosphate, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
micelle2200 uM [U-15N] core AthTatA, 120 mM NA DHPC-d22, 20 mM NA sodium phosphate, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMcore AthTatA[U-13C; U-15N]1
120 mMDHPC-d22NA1
20 mMsodium phosphateNA1
200 uMcore AthTatA[U-15N]2
120 mMDHPC-d22NA2
20 mMsodium phosphateNA2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE6004
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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