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- PDB-7bgh: Solution structure of the chloroplast outer envelope channel OEP21 -

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Basic information

Entry
Database: PDB / ID: 7bgh
TitleSolution structure of the chloroplast outer envelope channel OEP21
ComponentsOuter envelope pore protein 21, chloroplastic
KeywordsMEMBRANE PROTEIN / anion channel beta-barrel triosephosphate ATP
Function / homologyetioplast membrane / Outer envelope pore protein 21 / : / voltage-gated monoatomic anion channel activity / porin activity / pore complex / regulation of monoatomic anion transport / Outer envelope pore protein 21, chloroplastic
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodSOLUTION NMR / simulated annealing
AuthorsHagn, F. / Haeusler, E.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Helmholtz AssociationVG-NG-1035 Germany
European Commission291763European Union
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21.
Authors: Gunsel, U. / Klopfer, K. / Hausler, E. / Hitzenberger, M. / Bolter, B. / Sperl, L.E. / Zacharias, M. / Soll, J. / Hagn, F.
History
DepositionJan 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Outer envelope pore protein 21, chloroplastic


Theoretical massNumber of molelcules
Total (without water)22,0991
Polymers22,0991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Homodimerization or higher oligomers
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13200 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer envelope pore protein 21, chloroplastic / Chloroplastic outer envelope pore protein of 21 kDa / gOEP21


Mass: 22098.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal His-10 Tag with a two-amino-acid spacer (LE).
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: OEP21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SM57

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N TROSY HSQC
121isotropic33D HNCA
131isotropic33D HN(CA)CB
141isotropic33D HNCO
1101isotropic33D HN(CA)CO
151isotropic33D HN(CO)CA
161isotropic33D 1H-15N NOESY
1133isotropic22D 1H-15N TROSY HSQC
1113isotropic22D 1H-13C HMQC
173isotropic23D 1H-15N NOESY
183isotropic23D 1H-13C NOESY aliphatic
193isotropic33D 13C-13C NOESY aliphatic
1123isotropic33D 13C-15N NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle10.4 mM [U-13C; U-15N; U-2H] OEP21, 300 mM [U-100% 2H] LDAO, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 0.5 mM EDTA, 95% H2O/5% D2O2H,13C,15N-labeled OEP21 in deuterated LDAO micellesDCN95% H2O/5% D2O
micelle30.4 mM [ U-15N; U-2H],ILVAFY OEP21, 300 mM [U-100% 2H] LDAO, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 0.5 mM EDTA, 95% H2O/5% D2O2H,15N-labeled OEP21 with stereospecific ILVA 1H,13C-methyl labeled amino acids: pro-S for Leu and Val, delta1 for Ile, beta for Ala, including 1H,15N-labeled aromatic amino acids Phe and Tyr in deuterated LDAO micellesILVAFY95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMOEP21[U-13C; U-15N; U-2H]1
300 mMLDAO[U-100% 2H]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
0.5 mMEDTAnatural abundance1
0.4 mMOEP21[ U-15N; U-2H],ILVAFY3
300 mMLDAO[U-100% 2H]3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
5 mMDTTnatural abundance3
0.5 mMEDTAnatural abundance3
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9002
Bruker AVANCE III HDBrukerAVANCE III HD8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
hmsISTWagner Lab, Harvard Medical Schoolprocessing
NMRFAM-SPARKYUniv of Wisconsinchemical shift assignment
NMRFAM-SPARKYUniv of Wisconsinpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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