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- PDB-6uxe: Structure of the human mitochondrial desulfurase complex Nfs1-ISC... -

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Basic information

Entry
Database: PDB / ID: 6uxe
TitleStructure of the human mitochondrial desulfurase complex Nfs1-ISCU2(M140I)-ISD11 with E.coli ACP1 at 1.57 A resolution showing flexibility of N terminal end of ISCU2
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / human mitochondrial cysteine desulfurase complex
Function / homology
Function and homology information


iron-sulfur cluster chaperone activity / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / Complex III assembly / positive regulation of mitochondrial electron transport, NADH to ubiquinone ...iron-sulfur cluster chaperone activity / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / 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 / lipid biosynthetic process / acyl binding / acyl carrier activity / iron-sulfur cluster binding / phosphopantetheine binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / 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 / structural molecule activity / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
LYRM4, LYR domain / : / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / 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 ...LYRM4, LYR domain / : / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / 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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-EDT / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / Acyl carrier protein / Iron-sulfur cluster assembly enzyme ISCU ...Chem-8Q1 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-EDT / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / 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 / molecular replacement / Resolution: 1.57 Å
AuthorsBoniecki, M.T. / Cygler, M.
CitationJournal: To Be Published
Title: The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis
Authors: Freibert, S.A. / Boniecki, M.T. / Shulz, V. / Wilbrecht, C. / Krapoth, N. / Muhlenhoff, U. / Stehling, O. / Cygler, M. / Lill, R.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,65283
Polymers80,0254
Non-polymers7,62679
Water7,026390
1
A: Cysteine desulfurase, mitochondrial
B: LYR motif-containing protein 4
C: Acyl carrier protein
D: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)175,304166
Polymers160,0518
Non-polymers15,253158
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area18130 Å2
ΔGint-110 kcal/mol
Surface area52720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.410, 86.410, 245.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Cysteine desulfurase, mitochondrial


Mass: 45081.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Plasmid: pET15 / Details (production host): no tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / 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 / Plasmid: pACYC-1 Duet / Details (production host): no tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q9HD34
#3: Protein Acyl carrier protein / ACP


Mass: 8514.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP, ECS88_1108 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: B7MJ81, UniProt: P0A6A8*PLUS
#4: Protein Iron-sulfur cluster assembly enzyme ISCU, mitochondrial / NifU-like N-terminal domain-containing protein / NifU-like protein


Mass: 15666.080 Da / Num. of mol.: 1 / Mutation: M140I
Source method: isolated from a genetically manipulated source
Details: Met140Ile mutant / Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU, NIFUN / Plasmid: pET24b / Details (production host): CHIS tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q9H1K1

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Non-polymers , 13 types, 469 molecules

#5: 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
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: 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
#11: 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
#12: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#13: 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
#14: 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 / Feature type: SUBJECT OF INVESTIGATION
#15: 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
#16: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 288 K / Method: vapor diffusion / Details: 0.1 M MES pH 6.0-6.5, 22% PEG400 / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.57→48.98 Å / Num. obs: 130413 / % possible obs: 99.98 % / Redundancy: 14.5 % / Biso Wilson estimate: 21.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.59
Reflection shellResolution: 1.57→1.626 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 12829 / CC1/2: 0.725 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5USR

5usr


Resolution: 1.57→48.98 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.34
RfactorNum. reflection% reflection
Rfree0.1796 6521 5 %
Rwork0.1564 --
obs0.1576 130413 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.63 Å2 / Biso mean: 31.9843 Å2 / Biso min: 9.83 Å2
Refinement stepCycle: final / Resolution: 1.57→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5183 0 494 390 6067
Biso mean--57.52 36.98 -
Num. residues----681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.57-1.58780.26832130.2494041
1.5878-1.60650.27532140.24764069
1.6065-1.62610.26432140.23154073
1.6261-1.64670.25382120.22464036
1.6467-1.66840.23812160.20944092
1.6684-1.69120.2412150.20044093
1.6912-1.71540.22662130.18764038
1.7154-1.7410.21772160.18214102
1.741-1.76820.20512150.16874092
1.7682-1.79720.16882160.16154097
1.7972-1.82820.19932140.15914066
1.8282-1.86140.1852150.15724087
1.8614-1.89720.18052140.15434069
1.8972-1.9360.16472160.14924099
1.936-1.9780.16742160.15294116
1.978-2.02410.17262150.14124077
2.0241-2.07470.17922170.15324127
2.0747-2.13080.17372160.14824092
2.1308-2.19350.17882170.14544134
2.1935-2.26430.19342170.14964112
2.2643-2.34520.16622170.15074140
2.3452-2.43910.19332170.15494124
2.4391-2.55010.17332190.15214161
2.5501-2.68450.18792190.15034145
2.6845-2.85270.17862180.15294153
2.8527-3.07290.16552210.15324196
3.0729-3.38210.16932210.15324196
3.3821-3.87130.16992230.14214230
3.8713-4.87680.14542260.13774302
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)
10.45940.01240.18820.1998-0.05250.91410.0074-0.038-0.0473-00.0149-0.04260.01330.2016-0.0140.09840.00070.00590.1607-0.00160.156941.62662.79274
22.03861.1272-0.32253.283-0.75281.5329-0.05940.08090.1273-0.10160.0522-0.014-0.23680.0686-0.02930.15230.0091-0.00670.0981-0.00850.135224.2485.57667.144
34.6404-0.51370.05551.17941.03322.84930.0624-0.7590.47540.7080.00010.0741-0.3623-0.3955-0.04190.70860.01550.09060.3463-0.03230.327518.423102.61977.739
41.58820.3535-0.37012.7777-0.59923.5313-0.074-0.131-0.53150.02670.05760.14220.6322-0.1445-0.05850.2348-0.00330.02380.27670.05020.289325.20747.756108.161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 55:455 OR RESID 501:501 ) )A55 - 455
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 55:455 OR RESID 501:501 ) )A501
3X-RAY DIFFRACTION2( CHAIN B AND RESID 2:86 )B2 - 86
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 2:76 OR RESID 301:301 ) )C2 - 76
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 2:76 OR RESID 301:301 ) )C301
6X-RAY DIFFRACTION4( CHAIN D AND RESID 34:159 )D34 - 159

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