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- PDB-5wkp: Crystal Structure of the Human mitochondrial Cysteine Desulfurase... -

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Basic information

Entry
Database: PDB / ID: 5wkp
TitleCrystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and Iron-Sulfur Cluster Scaffold Protein ISCU1, and E. coli ACP1 protein at 3.15A
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / Human mitochondrial cysteine desulfurse LYR Motif containing protein 4 Iron-Sulfur Cluster Scaffold Protein ISCU1 Acyl Carrier Protein 1 (E.coli)
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 biosynthetic process / lipid A biosynthetic process / iron-sulfur cluster assembly / 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 / 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 / Phosphopantetheine attachment site. / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / 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 / Resolution: 3.15 Å
AuthorsBoniecki, M.T. / Cygler, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.
Authors: Boniecki, M.T. / Freibert, S.A. / Muhlenhoff, U. / Lill, R. / Cygler, M.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
E: Cysteine desulfurase, mitochondrial
F: LYR motif-containing protein 4
G: Acyl carrier protein
H: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,97012
Polymers161,3948
Non-polymers1,5764
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-111 kcal/mol
Surface area51520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.360, 123.290, 151.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Cysteine desulfurase, mitochondrial


Mass: 45081.578 Da / Num. of mol.: 2 / Fragment: UNP residues 56-457
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.: 2
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.: 2
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, UniProt: P0A6A8*PLUS
#4: Protein Iron-sulfur cluster assembly enzyme ISCU, mitochondrial / NifU-like N-terminal domain-containing protein / NifU-like protein


Mass: 16337.819 Da / Num. of mol.: 2
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 , 2 types, 4 molecules

#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: 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.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS

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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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MES pH 7 15 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.15→49.389 Å / Num. obs: 32516 / % possible obs: 99.8 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 15.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVM, 3LVL, 2FAE

3lvm

3lvl

2fae


Resolution: 3.15→49.389 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 2000 6.15 %
Rwork0.1862 --
obs0.1897 32499 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→49.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9788 0 98 0 9886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210046
X-RAY DIFFRACTIONf_angle_d0.56213657
X-RAY DIFFRACTIONf_dihedral_angle_d14.2426055
X-RAY DIFFRACTIONf_chiral_restr0.0421619
X-RAY DIFFRACTIONf_plane_restr0.0031761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.22890.34031380.29982089X-RAY DIFFRACTION97
3.2289-3.31610.33251390.24712139X-RAY DIFFRACTION100
3.3161-3.41370.3171420.22292160X-RAY DIFFRACTION100
3.4137-3.52390.2581410.21462153X-RAY DIFFRACTION100
3.5239-3.64980.27471420.20582159X-RAY DIFFRACTION100
3.6498-3.79580.24851390.18142134X-RAY DIFFRACTION100
3.7958-3.96850.21571440.1732174X-RAY DIFFRACTION100
3.9685-4.17770.23131400.16872143X-RAY DIFFRACTION100
4.1777-4.43920.21371440.16442200X-RAY DIFFRACTION100
4.4392-4.78170.22241430.15162184X-RAY DIFFRACTION100
4.7817-5.26250.22361430.16392187X-RAY DIFFRACTION100
5.2625-6.02280.25021450.20062207X-RAY DIFFRACTION100
6.0228-7.58370.24291460.20542237X-RAY DIFFRACTION100
7.5837-49.39530.22551540.1722333X-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)
11.2311-0.287-0.5511.1761-0.26583.1062-0.17160.1384-0.2476-0.2619-0.00310.01770.423-0.20340.11260.4601-0.07020.110.4237-0.04020.520846.21836.681656.2831
20.3821-0.50670.30331.96730.44150.9228-0.001-0.1408-0.2197-0.1337-0.0163-0.21450.50350.04930.03070.8996-0.08050.26360.74940.07980.955444.434120.516280.7909
30.9933-0.12710.09551.80280.35320.89240.4282-0.3702-0.59790.6631-0.0633-0.01991.0946-0.3495-0.221.2994-0.20340.13020.64850.24051.362839.4770.968885.8601
40.5697-0.1840.41520.43940.30730.6967-0.55740.7757-0.1025-0.7080.31560.2262-0.4030.12260.00021.1092-0.4938-0.24661.9014-0.17691.64868.157632.070738.8475
51.62680.08770.24321.85090.11572.2608-0.1759-0.10250.1449-0.00220.01350.0206-0.2613-0.28030.17290.36910.0432-0.00310.4319-0.0520.411742.400565.009876.777
61.30441.06420.96522.63730.79472.2432-0.1125-0.270.18440.1734-0.03760.29760.0665-0.46010.11090.58230.02530.17690.71290.0250.609427.529547.49595.774
70.79250.75070.24472.28550.351.3205-0.1548-0.0682-0.35940.40310.15420.14370.5333-0.5909-0.01020.7596-0.04380.1131.0456-0.10180.630624.68447.2176116.1588
83.973-1.0952-0.14362.5305-0.66492.52520.00510.3553-0.2632-0.2399-0.03380.01160.30530.2023-0.07340.78290.0163-0.17760.7012-0.0310.631780.357870.521195.697
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 5:85 )B5 - 85
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 4:75 OR RESID 301:301 ) )C4 - 75
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 4:75 OR RESID 301:301 ) )C301
6X-RAY DIFFRACTION4( CHAIN D AND RESID 15:132 )D15 - 132
7X-RAY DIFFRACTION5( CHAIN E AND ( RESID 54:456 OR RESID 501:501 ) )E54 - 456
8X-RAY DIFFRACTION5( CHAIN E AND ( RESID 54:456 OR RESID 501:501 ) )E501
9X-RAY DIFFRACTION6( CHAIN F AND RESID 4:85 )F4 - 85
10X-RAY DIFFRACTION7( CHAIN G AND ( RESID 3:73 OR RESID 301:301 ) )G3 - 73
11X-RAY DIFFRACTION7( CHAIN G AND ( RESID 3:73 OR RESID 301:301 ) )G301
12X-RAY DIFFRACTION8( CHAIN H AND RESID 10:135 )H10 - 135

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