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- PDB-1ly7: The solution structure of the the c-terminal domain of frataxin, ... -

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Basic information

Entry
Database: PDB / ID: 1ly7
TitleThe solution structure of the the c-terminal domain of frataxin, the protein responsible for friedreich ataxia
Componentsfrataxin
KeywordsUNKNOWN FUNCTION / alpha-beta
Function / homology
Function and homology information


positive regulation of lyase activity / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching ...positive regulation of lyase activity / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching / Mitochondrial protein import / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / oxidative phosphorylation / response to iron ion / [2Fe-2S] cluster assembly / heme biosynthetic process / adult walking behavior / negative regulation of multicellular organism growth / organ growth / iron-sulfur cluster assembly / muscle cell cellular homeostasis / ferroxidase / negative regulation of release of cytochrome c from mitochondria / protein autoprocessing / ferroxidase activity / ferric iron binding / protein maturation / enzyme activator activity / iron ion transport / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cellular response to hydrogen peroxide / intracellular iron ion homeostasis / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / cytosol
Similarity search - Function
Frataxin/CyaY / Frataxin / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily ...Frataxin/CyaY / Frataxin / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Frataxin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMusco, G. / Stier, G. / Kolmerer, B. / Adinolfi, S. / Martin, S. / Frenkiel, T. / Gibson, T. / Pastore, A.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Towards a structural understanding of Friedreich's ataxia: the solution structure of frataxin
Authors: Musco, G. / Stier, G. / Kolmerer, B. / Adinolfi, S. / Martin, S. / Frenkiel, T. / Gibson, T. / Pastore, A.
#1: Journal: J.BIOMOL.NMR / Year: 1999
Title: Assignment of the 1H, 15N, and 13C resonances of the C-terminal domain of frataxin, the protein responsible for friedreich ataxia
Authors: Musco, G. / De Tommasi, T. / Stier, G. / Kolmerer, B. / Bottomley, M. / Adinolfi, S. / Muskett, F.W. / Gibson, T.J. / Frenkiel, T.A. / Pastore, A.
History
DepositionJun 7, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJun 26, 2002ID: 1DLX
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: frataxin


Theoretical massNumber of molelcules
Total (without water)13,5061
Polymers13,5061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein frataxin / Friedreich's ataxia protein / Fxn


Mass: 13505.929 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (91-210)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: Q16595

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1 MM FRATAXIN. U-15N 10 MM PHOSPHATE BUFFER (PH 6.8)90% H2O, 10% D2O
Solvent system: h2o
Sample conditionsIonic strength: 10 mM phosphate / pH: 6.8 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002
Bruker DMXBrukerDMX8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7Delaglio et al.processing
XEASY1.2Glaserdata analysis
ARIA1Nilges et al.structure solution
ARIA1Nilges et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ARIA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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