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- SASDDD3: Human mitochondrial cysteine desulfurase-ISCU-Frataxin (NFS1, ISD... -

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Basic information

Entry
Database: SASBDB / ID: SASDDD3
SampleHuman mitochondrial cysteine desulfurase-ISCU-Frataxin (NFS1, ISD11 and Acp heterodimer complex)
  • Cysteine desulfurase, mitochondrial (protein), NFS1, Homo sapiens
  • LYR motif-containing protein 4 (protein), ISD11, Homo sapiens
  • Acyl carrier protein (protein), Escherichia coli (strain K12)
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (protein), ISCU, Homo sapiens
  • Frataxin, mitochondrial (protein), FXN, Homo sapiens
Function / homology
Function and homology information


positive regulation of lyase activity / iron-sulfur cluster chaperone activity / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / proprioception / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity ...positive regulation of lyase activity / iron-sulfur cluster chaperone activity / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / proprioception / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / Complex III assembly / iron chaperone activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / 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 / lipid A biosynthetic process / iron-sulfur cluster assembly / muscle cell cellular homeostasis / lipid biosynthetic process / ferroxidase / negative regulation of release of cytochrome c from mitochondria / acyl binding / acyl carrier activity / protein autoprocessing / ferroxidase activity / iron-sulfur cluster binding / phosphopantetheine binding / 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 / fatty acid biosynthetic process / pyridoxal phosphate binding / Maturation of replicase proteins / molecular adaptor activity / intracellular iron ion homeostasis / nuclear body / mitochondrial matrix / iron ion binding / response to xenobiotic stimulus / lipid binding / centrosome / negative regulation of apoptotic process / structural molecule activity / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
LYRM4, LYR domain / : / Frataxin / ISC system FeS cluster assembly, IscU scaffold / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain ...LYRM4, LYR domain / : / Frataxin / ISC system FeS cluster assembly, IscU scaffold / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Frataxin/CyaY superfamily / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Pyridoxal phosphate-dependent transferase, small domain / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Acyl carrier protein / Frataxin, mitochondrial / Iron-sulfur cluster assembly enzyme ISCU / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (strain K12) (bacteria)
CitationJournal: Structure / Year: 2018
Title: Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering.
Authors: Kai Cai / Ronnie O Frederick / Hesam Dashti / John L Markley /
Abstract: Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for ...Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for assembling other components of the biosynthetic machinery, including ISCU, frataxin, and ferredoxin. The human mitochondrial cysteine desulfurase complex consists of two copies each of NFS1, ISD11, and acyl carrier protein. We describe results from chemical crosslinking coupled with tandem mass spectrometry and small-angle X-ray scattering studies that are consistent with a closed NFS1 dimer rather than an open one for both the cysteine desulfurase-ISCU and cysteine desulfurase-ISCU-frataxin complexes. We present a structural model for the cysteine desulfurase-ISCU-frataxin complex derived from chemical crosslinking restraints in conjunction with the recent crystal structure of the cysteine desulfurase-ISCU-zinc complex and distance constraints from nuclear magnetic resonance.
Contact author
  • Kai Cai (University of Wisconsin-Madison, Madison, WI, USA)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #1776
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 4.937284 / P-value: 0.000004
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Human mitochondrial cysteine desulfurase-ISCU-Frataxin (NFS1, ISD11 and Acp heterodimer complex)
Specimen concentration: 2.00-10.00 / Entity id: 958 / 959 / 960 / 961 / 962
BufferName: 20 mM HEPES, 150 mM NaCl, 5 mM TCEP / pH: 7.5 / Comment: HNT Buffer
Entity #958Name: NFS1 / Type: protein / Description: Cysteine desulfurase, mitochondrial / Formula weight: 44.913 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q9Y697
Sequence: GPVLRPLYMD VQATTPLDPR VLDAMLPYLI NYYGNPHSRT HAYGWESEAA MERARQQVAS LIGADPREII FTSGATESNN IAIKGVARFY RSRKKHLITT QTEHKCVLDS CRSLEAEGFQ VTYLPVQKSG IIDLKELEAA IQPDTSLVSV MTVNNEIGVK QPIAEIGRIC ...Sequence:
GPVLRPLYMD VQATTPLDPR VLDAMLPYLI NYYGNPHSRT HAYGWESEAA MERARQQVAS LIGADPREII FTSGATESNN IAIKGVARFY RSRKKHLITT QTEHKCVLDS CRSLEAEGFQ VTYLPVQKSG IIDLKELEAA IQPDTSLVSV MTVNNEIGVK QPIAEIGRIC SSRKVYFHTD AAQAVGKIPL DVNDMKIDLM SISGHKIYGP KGVGAIYIRR RPRVRVEALQ SGGGQERGMR SGTVPTPLVV GLGAACEVAQ QEMEYDHKRI SKLSERLIQN IMKSLPDVVM NGDPKHHYPG CINLSFAYVE GESLLMALKD VALSSGSACT SASLEPSYVL RAIGTDEDLA HSSIRFGIGR FTTEEEVDYT VEKCIQHVKR LREMSPLWEM VQDGIDLKSI KWTQH
Entity #959Name: ISD11 / Type: protein / Description: LYR motif-containing protein 4 / Formula weight: 11.581 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q9HD34
Sequence:
MAASSRAQVL SLYRAMLRES KRFSAYNYRT YAVRRIRDAF RENKNVKDPV EIQTLVNKAK RDLGVIRRQV HIGQLYSTDK LIIENRDMPR THHHHHH
Entity #960Type: protein / Description: Acyl carrier protein / Formula weight: 11.5 / Num. of mol.: 2 / Source: Escherichia coli (strain K12) / References: UniProt: P0A6A8
Sequence:
PspP0A6A8A CPECOLIAcy lcarrierpr oteinOSEsc herichiaco li(strainK12)GNacpPP E1SV2MSTIE ERVKKIIGEQ LGVKQEEVTN NASFVEDLGA DSLDTVELVM ALEEEFDTEI PDEEAEKITT VQAAIDYING HQA
Entity #961Name: ISCU / Type: protein
Description: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
Formula weight: 14.655 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q9H1K1
Sequence:
RLYHKKVVDH YENPRNVGSL DKTSKNVGTG LVGAPACGDV MKLQIQVDEK GKIVDARFKT FGCGSAIASS SLATEWVKGK TVEEALTIKN TDIAKELCLP PVKLHCSMLA EDAIKAALAD YKLKQEPKKG EAEKK
Entity #962Name: FXN / Type: protein / Description: Frataxin, mitochondrial / Formula weight: 14.268 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q16595
Sequence:
SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS SGPKRYDWTG KNWVYSHDGV SLHELLAAEL TKALKTKLDL SSLAYSGKDA

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Experimental information

BeamInstrument name: NMRFAM Bruker Nanostar / City: Madison, WI / 国: USA / Type of source: X-ray in house / Wavelength: 0.15418 Å / Dist. spec. to detc.: 1 mm
DetectorName: VÅNTEC-2000 / Type: MikroGap / Pixsize x: 200 mm
Scan
Title: Human mitochondrial cysteine desulfurase-ISCU-Frataxin (NFS1, ISD11 and Acp heterodimer complex)
Measurement date: Apr 18, 2017 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 3600 sec. / Number of frames: 4 / Unit: 1/A /
MinMax
Q0 0.256
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 125 /
MinMax
Q0.01707 0.1934
P(R) point12 136
R0 143.8
Result
Type of curve: single_conc
Comments: The solution SAXS study of cysteine desulfurase complex containing ISCU and Frataxin
ExperimentalPorod
MW175 kDa-
Volume-287 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I01941 8 1933.33 9.7
Radius of gyration, Rg4.21 nm0.05 4.14 nm0.12

MinMaxError
D-14.38 0.05
Guinier point10 23 -

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