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- PDB-8trw: Structure of human LIAS -

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Basic information

Entry
Database: PDB / ID: 8trw
TitleStructure of human LIAS
ComponentsLipoyl synthase, mitochondrial
KeywordsBIOSYNTHETIC PROTEIN / Lipoyl synthase / LIAS
Function / homology
Function and homology information


lipoyl synthase / lipoate synthase activity / lipoate biosynthetic process / Protein lipoylation / neural tube closure / 4 iron, 4 sulfur cluster binding / response to oxidative stress / response to lipopolysaccharide / mitochondrial matrix / inflammatory response ...lipoyl synthase / lipoate synthase activity / lipoate biosynthetic process / Protein lipoylation / neural tube closure / 4 iron, 4 sulfur cluster binding / response to oxidative stress / response to lipopolysaccharide / mitochondrial matrix / inflammatory response / mitochondrion / metal ion binding
Similarity search - Function
Lipoyl synthase, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / Lipoyl synthase / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / IRON/SULFUR CLUSTER / Lipoyl synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsEsakova, O.A. / Warui, D.M. / Neti, S.S. / Alumasa, J.N. / Booker, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-122595 United States
National Science Foundation (NSF, United States)MCB1716686 United States
Howard Hughes Medical Institute (HHMI)SJB United States
CitationJournal: To Be Published
Title: Structural basis for the mechanism of the human lipoyl synthase (LIAS) and its complex with the H-protein
Authors: Esakova, O.A. / Warui, D.M. / Neti, S.S. / Alumasa, J.N. / Booker, S.J.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoyl synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8406
Polymers41,5441
Non-polymers1,2965
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.353, 88.789, 108.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

21A-725-

HOH

31A-729-

HOH

41A-802-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lipoyl synthase, mitochondrial


Mass: 41543.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIAS / Production host: Escherichia (bacteria) / References: UniProt: O43766
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 375 molecules

#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.2 M Sodium sulfate, 30% (w/v) PEG 3350, 3% (w/v) D-(+)-trehalose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 199757 / % possible obs: 98.8 % / Redundancy: 4.1 % / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 21
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 2402 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→27.08 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 3168 4.22 %
Rwork0.1521 --
obs0.1532 75051 78.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 36 371 2746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012548
X-RAY DIFFRACTIONf_angle_d1.1823482
X-RAY DIFFRACTIONf_dihedral_angle_d24.084990
X-RAY DIFFRACTIONf_chiral_restr0.079393
X-RAY DIFFRACTIONf_plane_restr0.013440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.2332590.25021322X-RAY DIFFRACTION33
1.56-1.580.2933700.23461632X-RAY DIFFRACTION42
1.58-1.610.1904800.21321794X-RAY DIFFRACTION45
1.61-1.640.1952890.19592024X-RAY DIFFRACTION51
1.64-1.670.1897950.18062200X-RAY DIFFRACTION55
1.67-1.70.20841020.17582344X-RAY DIFFRACTION59
1.7-1.730.18431060.16992547X-RAY DIFFRACTION64
1.73-1.770.17331240.1542848X-RAY DIFFRACTION72
1.77-1.810.17921420.15483139X-RAY DIFFRACTION79
1.81-1.860.15731530.15133347X-RAY DIFFRACTION85
1.86-1.910.16781490.15163517X-RAY DIFFRACTION89
1.91-1.960.14931570.14183654X-RAY DIFFRACTION93
1.96-2.030.17821640.14513754X-RAY DIFFRACTION95
2.03-2.10.1961700.15253865X-RAY DIFFRACTION97
2.1-2.180.17131760.14473838X-RAY DIFFRACTION98
2.18-2.280.18721660.14953874X-RAY DIFFRACTION97
2.28-2.40.18331700.143774X-RAY DIFFRACTION97
2.4-2.550.16321720.15323838X-RAY DIFFRACTION97
2.55-2.750.19981700.15963786X-RAY DIFFRACTION96
2.75-3.030.19431720.15513813X-RAY DIFFRACTION96
3.03-3.460.17741630.15143743X-RAY DIFFRACTION95
3.46-4.360.18481670.13513724X-RAY DIFFRACTION94
4.36-27.080.16751520.15243506X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 46.0838 Å / Origin y: 15.792 Å / Origin z: 36.7668 Å
111213212223313233
T0.0954 Å2-0.0143 Å2-0.0025 Å2-0.0771 Å20.0177 Å2--0.0871 Å2
L1.4306 °2-0.2132 °2-0.1237 °2-0.5425 °2-0.1326 °2--0.7364 °2
S-0.0245 Å °-0.0473 Å °-0.0699 Å °0.0094 Å °0.0106 Å °-0.0287 Å °0.0448 Å °0.0141 Å °0.0073 Å °
Refinement TLS groupSelection details: all

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