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- PDB-6zdb: NMR structural analysis of yeast Cox13 reveals its C-terminus in ... -

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Basic information

Entry
Database: PDB / ID: 6zdb
TitleNMR structural analysis of yeast Cox13 reveals its C-terminus in interaction with ATP
ComponentsCytochrome c oxidase subunit 13, mitochondrial
KeywordsSTRUCTURAL PROTEIN / membrane protein / solution structure / ATP/ADP
Function / homology
Function and homology information


mitochondrial respirasome assembly / : / mitochondrial electron transport, cytochrome c to oxygen / enzyme regulator activity / proton transmembrane transport / aerobic respiration / oxidoreductase activity / mitochondrion
Similarity search - Function
Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa
Similarity search - Domain/homology
Cytochrome c oxidase subunit 13, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsShu, Z. / Pontus, P. / Peter, B. / Lena, M. / Pia, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Bmc Biol. / Year: 2021
Title: NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP.
Authors: Zhou, S. / Pettersson, P. / Bjorck, M.L. / Dawitz, H. / Brzezinski, P. / Maler, L. / Adelroth, P.
History
DepositionJun 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 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
A: Cytochrome c oxidase subunit 13, mitochondrial
B: Cytochrome c oxidase subunit 13, mitochondrial


Theoretical massNumber of molelcules
Total (without water)30,0922
Polymers30,0922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area730 Å2
ΔGint-4 kcal/mol
Surface area29250 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase polypeptide VIa


Mass: 15046.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: COX13, YGL191W, G1341 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P32799

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N TROSY HSQC
122isotropic23D backbone experiments
132isotropic23D sidechain experiments
142isotropic23D 15N-NOESY
152isotropic23D 13C-NOESY
163isotropic23D 15N-filtered/edited-NOESY
173isotropic23D 13C-filtered/edited-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.5 mM [U-15N] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O15N_Cox1390% H2O/10% D2O
micelle20.5 mM [U-13C; U-15N] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O[15N, 13C]_Cox1390% H2O/10% D2O
micelle30.5 mM 50%[15N, 13C] mixed with 50% [14N, 12C] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O50%[15N, 13C] mixed with 50% [14N, 12C]_Cox13_Cox1390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCytochrome c oxidase subunit 13, Cox13[U-15N]1
0.5 mMCytochrome c oxidase subunit 13, Cox13[U-13C; U-15N]2
0.5 mMCytochrome c oxidase subunit 13, Cox1350%[15N, 13C] mixed with 50% [14N, 12C]3
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 313.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
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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