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- PDB-8tvt: Structure of human Cysteine desulfurase Nfs1 with L-propargylglyc... -

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Basic information

Entry
Database: PDB / ID: 8tvt
TitleStructure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2
Components
  • Acyl carrier protein
  • Cysteine desulfurase
  • Iron-sulfur cluster assembly enzyme ISCU
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / Nfs1 / PG-PLP bound
Function / homology
Function and homology information


negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / iron incorporation into metallo-sulfur cluster / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / positive regulation of mitochondrial electron transport, NADH to ubiquinone / Maturation of TCA enzymes and regulation of TCA cycle ...negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / iron incorporation into metallo-sulfur cluster / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / positive regulation of mitochondrial electron transport, NADH to ubiquinone / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / lipid A biosynthetic process / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / iron-sulfur cluster binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / Maturation of replicase proteins / molecular adaptor activity / intracellular iron ion homeostasis / nuclear body / mitochondrial matrix / iron ion binding / centrosome / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
LYRM4, LYR domain / : / ISC system FeS cluster assembly, IscU scaffold / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain ...LYRM4, LYR domain / : / ISC system FeS cluster assembly, IscU scaffold / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / 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 / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-8Q1 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-EDT / L-Propargylglycine / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / Iron-sulfur cluster assembly enzyme ISCU ...Chem-8Q1 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-EDT / L-Propargylglycine / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / Iron-sulfur cluster assembly enzyme ISCU / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCygler, M. / Boniecki, M.T.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: D-Cysteine impairs tumor growth by inhibiting cysteine desulfurase NFS1
Authors: Zangari, J. / Stehling, O. / Freibert, S.A. / Rouaud, F. / Maundrell, K. / Beinier, V.S. / Ferre, M.S. / Vartholomaiou, E. / Montessuit, S. / Schulz, V. / Zuhra, K. / Ruiz, V.G. / Rudaz, S. ...Authors: Zangari, J. / Stehling, O. / Freibert, S.A. / Rouaud, F. / Maundrell, K. / Beinier, V.S. / Ferre, M.S. / Vartholomaiou, E. / Montessuit, S. / Schulz, V. / Zuhra, K. / Ruiz, V.G. / Rudaz, S. / Szabo, C. / Hanschke, S. / Tsukamoto, T. / Boniecki, M.T. / Cygler, M. / Lill, R. / Martinou, J.C.
History
DepositionAug 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
B: LYR motif-containing protein 4
C: Acyl carrier protein
D: Iron-sulfur cluster assembly enzyme ISCU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,13756
Polymers78,5344
Non-polymers5,60352
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.270, 86.270, 246.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Cysteine desulfurase


Mass: 44714.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y697, cysteine desulfurase
#2: Protein LYR motif-containing protein 4


Mass: 10763.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD34
#3: Protein Acyl carrier protein / ACP


Mass: 8443.187 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZKJ7
#4: Protein Iron-sulfur cluster assembly enzyme ISCU


Mass: 14612.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1K1

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Non-polymers , 14 types, 466 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-LPH / L-Propargylglycine / (2S)-2-aminopent-4-ynoic acid


Type: L-peptide linking / Mass: 113.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#12: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#13: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#14: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#15: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#16: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#17: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 22.5 % PEG 400 / Temp details: 15 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→48.95 Å / Num. obs: 63786 / % possible obs: 99.97 % / Redundancy: 7.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1379 / Net I/σ(I): 12.47
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.852 / Num. unique obs: 6269 / CC1/2: 0.818

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
AutoProcessdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.95 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 3190 5 %
Rwork0.1501 --
obs0.1519 63783 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 314 414 5966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019
X-RAY DIFFRACTIONf_angle_d1.632
X-RAY DIFFRACTIONf_dihedral_angle_d16.466947
X-RAY DIFFRACTIONf_chiral_restr0.1869
X-RAY DIFFRACTIONf_plane_restr0.019980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.3351370.28892595X-RAY DIFFRACTION100
2.03-2.060.2861360.24072580X-RAY DIFFRACTION100
2.06-2.10.24821360.19442592X-RAY DIFFRACTION100
2.1-2.130.2341360.17962579X-RAY DIFFRACTION100
2.13-2.170.19521360.15622587X-RAY DIFFRACTION100
2.17-2.210.21371370.16132611X-RAY DIFFRACTION100
2.21-2.260.23041360.16062575X-RAY DIFFRACTION100
2.26-2.310.22051370.15572599X-RAY DIFFRACTION100
2.31-2.360.18841360.14462585X-RAY DIFFRACTION100
2.36-2.420.17681370.13872616X-RAY DIFFRACTION100
2.42-2.480.16771380.13722617X-RAY DIFFRACTION100
2.48-2.560.18531370.14112598X-RAY DIFFRACTION100
2.56-2.640.19681380.13972627X-RAY DIFFRACTION100
2.64-2.730.17791370.14022604X-RAY DIFFRACTION100
2.73-2.840.18351390.14152630X-RAY DIFFRACTION100
2.84-2.970.18281390.14182645X-RAY DIFFRACTION100
2.97-3.130.19781380.14582631X-RAY DIFFRACTION100
3.13-3.330.17221390.14632645X-RAY DIFFRACTION100
3.33-3.580.17011400.14252658X-RAY DIFFRACTION100
3.58-3.940.1591410.12982679X-RAY DIFFRACTION100
3.94-4.510.15491420.12772696X-RAY DIFFRACTION100
4.51-5.680.16641440.14142739X-RAY DIFFRACTION100
5.69-8.940.19371540.17582905X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56560.00650.18810.2611-0.06471.09730.0101-0.0513-0.0580.00040.0212-0.05390.02670.221-0.01990.08550.00050.00610.15110.00170.161241.60362.58574.229
22.80891.2237-0.1974.0341-0.77941.9032-0.08770.06590.1216-0.10140.0666-0.0149-0.25120.0605-0.02660.15850.0232-0.01150.0916-0.01510.144224.29485.47467.155
34.7858-0.72530.21681.62211.41283.04770.0721-0.86180.48380.7660.04560.0325-0.3518-0.3752-0.110.75270.01150.10060.3478-0.03180.325618.563102.41477.673
42.2490.4844-0.41943.7433-0.33134.4023-0.0965-0.1738-0.6330.06310.02530.11360.6928-0.16570.00670.2217-0.00420.03660.2890.05510.304225.40647.579108.713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 55:454 OR RESID 503:503 ) )A55 - 454
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 55:454 OR RESID 503:503 ) )A503
3X-RAY DIFFRACTION2( CHAIN B AND RESID 2:85 )B2 - 85
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:76 OR RESID 301:301 ) )C3 - 76
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:76 OR RESID 301:301 ) )C301
6X-RAY DIFFRACTION4( CHAIN D AND RESID 34:159 )D34 - 159

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