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- PDB-6wi2: Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.... -

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Basic information

Entry
Database: PDB / ID: 6wi2
TitleStructure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present.
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


negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial iron-sulfur cluster assembly complex / positive regulation of aconitate hydratase activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone ...negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial iron-sulfur cluster assembly complex / positive regulation of aconitate hydratase activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / cysteine desulfurase / cysteine desulfurase activity / iron-sulfur cluster assembly complex / Mo-molybdopterin cofactor biosynthetic process / [2Fe-2S] cluster assembly / acyl binding / iron-sulfur cluster assembly / lipid biosynthetic process / lipid A biosynthetic process / 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 / intracellular iron ion homeostasis / molecular adaptor activity / nuclear body / mitochondrial matrix / response to xenobiotic stimulus / iron ion binding / centrosome / lipid binding / 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 / Sufe protein. Chain: A - #10 / Cysteine desulfurase IscS / Sufe protein. Chain: A / 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. ...LYRM4, LYR domain / ISC system FeS cluster assembly, IscU scaffold / Sufe protein. Chain: A - #10 / Cysteine desulfurase IscS / Sufe protein. Chain: A / 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 / Chem-EDT / Chem-ETE / 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 / Resolution: 1.95 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
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)85,74662
Polymers79,9134
Non-polymers5,83258
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19820 Å2
ΔGint101 kcal/mol
Surface area29390 Å2
Unit cell
Length a, b, c (Å)86.430, 86.430, 246.120
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-665-

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 natural source / Source: (natural) 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: 15553.906 Da / Num. of mol.: 1
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 , 12 types, 461 molecules

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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


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


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#13: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID / Ethylenediaminetetraacetic 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-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion / 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: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→49.011 Å / Num. obs: 69004 / % possible obs: 99.97 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 22.62
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 6795 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W1D

6w1d


Resolution: 1.95→49.011 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.41
RfactorNum. reflection% reflection
Rfree0.1849 3450 5 %
Rwork0.1504 --
obs0.1521 68999 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.17 Å2 / Biso mean: 41.8796 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 1.95→49.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 376 403 6005
Biso mean--66.44 44.06 -
Num. residues----686
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.95-1.97670.2551370.19362595
1.9767-2.00490.20791360.16842590
2.0049-2.03490.20891340.16432547
2.0349-2.06670.2091360.16642587
2.0667-2.10050.21291370.16392586
2.1005-2.13680.19911330.16112537
2.1368-2.17560.18521370.15112610
2.1756-2.21750.20141380.14862605
2.2175-2.26270.19561340.15072559
2.2627-2.31190.1771360.14682579
2.3119-2.36570.18911360.14592578
2.3657-2.42490.18531370.14762603
2.4249-2.49040.17011370.14812607
2.4904-2.56370.19171370.14732609
2.5637-2.64640.18091380.14742610
2.6464-2.7410.18621360.14972593
2.741-2.85080.21380.15192621
2.8508-2.98050.1881390.15112650
2.9805-3.13760.17461370.14992594
3.1376-3.33410.19231400.15412660
3.3341-3.59150.19211390.15052641
3.5915-3.95280.18911410.13272670
3.9528-4.52440.16031410.13242690
4.5244-5.69890.16241440.14542726
5.6989-100.18921520.17422902
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)
10.75570.01390.25280.31310.01491.78610.0132-0.074-0.04530.01190.0311-0.06730.04670.3486-0.0280.1203-0.00460.00820.20950.00290.215141.567962.513174.2275
22.79021.3252-0.29014.3332-0.80442.3208-0.07330.12760.2122-0.11420.065-0.0141-0.3880.1024-0.02780.22080.0124-0.00750.1457-0.01160.202424.622485.645567.408
35.9611-1.1592-0.57782.09741.44224.75410.0529-0.96440.71641.00450.17450.1282-0.5422-0.452-0.18041.00710.01060.12860.4762-0.03840.500518.4877102.429777.9453
41.40810.5854-0.15633.0454-0.7875.3538-0.1032-0.3923-0.68510.17150.07690.29030.8075-0.1773-0.05470.3580.05170.06470.43140.12980.437825.367847.3802109.0445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 54 through 460)A54 - 460
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 85)B3 - 85
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 301)C2 - 301
4X-RAY DIFFRACTION4(chain 'D' and resid 36 through 159)D36 - 159

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