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- PDB-6lul: NMR structure and dynamics studies of yeast respiratory super-com... -

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Basic information

Entry
Database: PDB / ID: 6lul
TitleNMR structure and dynamics studies of yeast respiratory super-complex factor 2 in micelles
ComponentsRespiratory supercomplex factor 2, mitochondrial
KeywordsSTRUCTURAL PROTEIN / membrane protein / respiratory supercomplex factor
Function / homology
Function and homology information


mitochondrial cytochrome c oxidase assembly / : / positive regulation of protein-containing complex assembly / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile.
Similarity search - Domain/homology
Respiratory supercomplex factor 2, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsZhou, S. / Pontus, P. / Peter, B. / Maler, L. / Adelroth, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Structure / Year: 2021
Title: NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2.
Authors: Zhou, S. / Pettersson, P. / Huang, J. / Brzezinski, P. / Pomes, R. / Maler, L. / Adelroth, P.
History
DepositionJan 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Respiratory supercomplex factor 2, mitochondrial
A: Respiratory supercomplex factor 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)54,5202
Polymers54,5202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1200 Å2
ΔGint3 kcal/mol
Surface area41720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Respiratory supercomplex factor 2, mitochondrial / Altered inheritance of mitochondria protein 38


Mass: 27260.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: RCF2, AIM38, YNR018W, N3185 / Production host: Escherichia coli (E. coli) / References: UniProt: P53721

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic3TROSY-HSQC
123isotropic3Backbone Experiments
137isotropic3Side-chain Experiments
144isotropic3Side-chain Experiments
154isotropic3NOE Experiments
167isotropic3NOE Experiments
176isotropic3NOE Experiments

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.5 mM [U-99% 15N] Rcf2, 90% H2O/10% D2O15N_Rcf290% H2O/10% D2O
micelle20.5 mM 15N_2H Rcf2, 90% H2O/10% D2O15N_2H_Rcf290% H2O/10% D2O
micelle30.5 mM 15N_2H_13C Rcf2, 90% H2O/10% D2O15N_2H_13C_Rcf290% H2O/10% D2O
micelle40.5 mM 15N_50%-2H_13C Rcf2, 90% H2O/10% D2O15N_50%-2H_13C_Rcf290% H2O/10% D2O
micelle50.5 mM 15N_2H_13C-IVL Rcf2, 90% H2O/10% D2O15N_2H_13C-IVL_Rcf290% H2O/10% D2O
micelle60.5 mM 50% [13C, 15N] and 50% [12C, 14N] Rcf2, 90% H2O/10% D2O50% [13C, 15N] and 50% [12C, 14N]90% H2O/10% D2O
micelle70.5 mM [13C, 15N] Rcf2, 90% H2O/10% D2O13C_15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRcf2[U-99% 15N]1
0.5 mMRcf215N_2H2
0.5 mMRcf215N_2H_13C3
0.5 mMRcf215N_50%-2H_13C4
0.5 mMRcf215N_2H_13C-IVL5
0.5 mMRcf250% [13C, 15N] and 50% [12C, 14N]6
0.5 mMRcf2[13C, 15N]7
Sample conditionsIonic strength: 25 mM
Label: conditions_1, conditions_2, conditions_3, conditions_4, conditions_5, conditions_6, conditions_7
pH: 5 / Pressure: 1 atm / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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