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- PDB-7rtk: Structure of the (NIAU)2 complex with N-terminal mutation of ISCU... -

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Basic information

Entry
Database: PDB / ID: 7rtk
TitleStructure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A resolution
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / 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 / 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 / structural molecule activity / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
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. / ACP-like ...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. / ACP-like / Aminotransferase class V domain / Aminotransferase class-V / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / 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 / 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: 2.5 Å
AuthorsBoniecki, M.T. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
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
DepositionAug 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)85,52955
Polymers79,9954
Non-polymers5,53451
Water3,765209
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)171,059110
Polymers159,9918
Non-polymers11,068102
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)86.350, 86.350, 246.370
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-640-

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 / 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: 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 (E. coli) / References: UniProt: B7MJ81
#4: Protein Iron-sulfur cluster assembly enzyme ISCU, mitochondrial / NifU-like N-terminal domain-containing protein / NifU-like protein


Mass: 15636.033 Da / Num. of mol.: 1 / Mutation: Y35D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU, NIFUN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1K1

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Non-polymers , 13 types, 260 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#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
#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.: 209 / 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: 57.15 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES pH 5.5 22.5 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→49 Å / Num. obs: 33254 / % possible obs: 100 % / Redundancy: 12.924 % / Biso Wilson estimate: 44.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.157 / Χ2: 0.969 / Net I/σ(I): 14.26 / Num. measured all: 429761 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.6212.791.0112.754819428842860.8121.053100
2.62-2.7512.8540.7613.6348923380638060.9030.792100
2.75-2.8913.4460.5764.9745717340034000.9460.599100
2.89-3.0512.990.4296.4240998315831560.9650.44799.9
3.05-3.2313.2070.2979.0837997287728770.9840.309100
3.23-3.4312.8520.19812.6932311251425140.9930.206100
3.43-3.6613.3920.14317.4930307226322630.9960.149100
3.66-3.9212.90.10521.9725567198419820.9970.10999.9
3.92-4.2313.2310.08725.7823352176517650.9980.091100
4.23-4.5812.5890.07527.9118669148314830.9980.079100
4.58-513.2940.06830.9616803126412640.9990.071100
5-4912.180.06332.4454298446644580.9990.06699.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
AutoProcessphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXE

6uxe


Resolution: 2.5→49 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 1663 5 %
Rwork0.1688 31588 -
obs0.1711 33251 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.97 Å2 / Biso mean: 49.2438 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 2.5→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5151 0 358 210 5719
Biso mean--64.23 43.8 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035629
X-RAY DIFFRACTIONf_angle_d0.5767508
X-RAY DIFFRACTIONf_dihedral_angle_d11.885906
X-RAY DIFFRACTIONf_chiral_restr0.044841
X-RAY DIFFRACTIONf_plane_restr0.005944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.570.321350.263225722707
2.57-2.660.2781360.224325812717
2.66-2.750.27561360.194725752711
2.75-2.860.24541360.17525872723
2.86-2.990.22721360.176125952731
2.99-3.150.23311370.191425892726
3.15-3.350.26681370.190226002737
3.35-3.60.22161380.158726332771
3.61-3.970.18741380.144526272765
3.97-4.540.14821400.137226592799
4.54-5.720.18631420.151327002842
5.72-490.22291520.176628703022
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)
10.7690.00590.23570.435-0.05211.35810.0469-0.0179-0.0456-0.02130.022-0.03770.00540.2592-0.06930.2064-0.00570.0120.27310.00730.287841.68362.64974.148
23.13412.3096-1.04524.7036-1.1543.1912-0.07350.11180.0631-0.10360.0730.0254-0.37060.1089-0.01670.34320.0359-0.03970.2256-0.01560.328224.52685.55267.134
35.8811-1.0717-0.19872.02451.37024.11060.05-0.9160.86170.95740.19330.1553-0.745-0.6382-0.16651.09510.0420.12830.5239-0.03480.553518.54102.36577.683
42.61120.5267-0.39273.6668-0.77655.6246-0.1168-0.3136-0.66990.10990.00140.17480.8066-0.07280.02320.38430.02570.06860.46620.09710.477225.44247.322109.241
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 2:85 )B2 - 85
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 36:159 )D36 - 159

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