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- PDB-6nl3: Solution structure of human Coa6 -

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Basic information

Entry
Database: PDB / ID: 6nl3
TitleSolution structure of human Coa6
ComponentsCytochrome c oxidase assembly factor 6 homolog
KeywordsOXIDOREDUCTASE / mitochondrial proteins
Function / homology
Function and homology information


plasma membrane ATP synthesis coupled electron transport / respiratory chain complex IV assembly / respiratory chain complex IV / Mitochondrial protein import / mitochondrial ATP synthesis coupled electron transport / mitochondrial intermembrane space / copper ion binding / mitochondrion / RNA binding / nucleoplasm / plasma membrane
Similarity search - Function
Cytochrome c oxidase assembly factor 6 homolog / : / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
Cytochrome c oxidase assembly factor 6 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsNaik, M.T. / Soma, S. / Gohil, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111672 United States
CitationJournal: Cell Rep / Year: 2019
Title: COA6 Is Structurally Tuned to Function as a Thiol-Disulfide Oxidoreductase in Copper Delivery to Mitochondrial Cytochrome c Oxidase.
Authors: Soma, S. / Morgada, M.N. / Naik, M.T. / Boulet, A. / Roesler, A.A. / Dziuba, N. / Ghosh, A. / Yu, Q. / Lindahl, P.A. / Ames, J.B. / Leary, S.C. / Vila, A.J. / Gohil, V.M.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c oxidase assembly factor 6 homolog


Theoretical massNumber of molelcules
Total (without water)9,5871
Polymers9,5871
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 area6270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy
DetailsThe authors state that the protein is a homodimer according to gel filtration data and gives monodisperse NMR spectrum. They could not solve the dimer structure due to lack of inter-subunit NOEs and hence the structure has only a single chain.

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Components

#1: Protein Cytochrome c oxidase assembly factor 6 homolog


Mass: 9586.769 Da / Num. of mol.: 1 / Fragment: residues 47-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COA6, C1orf31 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5JTJ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D COSY
123isotropic12D TOCSY
1193isotropic22D NOESY
151isotropic12D 1H-15N HSQC
171isotropic13D 1H-15N TOCSY
132isotropic12D 1H-13C HSQC
142isotropic12D 1H-13C HSQC aromatic
1132isotropic13D HNCO
1122isotropic13D HN(CA)CO
1112isotropic13D HNCA
1102isotropic13D CBCA(CO)NH
192isotropic13D H(CCO)NH
182isotropic13D HBHA(CO)NH
162isotropic13D (H)CCH-COSY
1202isotropic12D-(HB)CB(CGCD)HD
1182isotropic23D 1H-15N NOESY
1172isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-15N] Coa6, 50 mM TRIS, 150 mM sodium chloride, 90% H2O/10% D2O15N-labeled Coa6N90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] Coa6, 50 mM TRIS, 150 mM sodium chloride, 90% H2O/10% D2O13C, 15N-labeled Coa6CN90% H2O/10% D2O
solution30.5 mM Coa6, 50 mM TRIS, 150 mM sodium chloride, 90% H2O/10% D2ONon-labeled Coa6Unlab90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCoa6[U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
0.5 mMCoa6[U-13C; U-15N]2
50 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
0.5 mMCoa6natural abundance3
50 mMTRISnatural abundance3
150 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 150 mM / Label: Condition1 / pH: 7.4 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing1
torsion angle dynamics2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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