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- PDB-9n51: Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase... -

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Basic information

Entry
Database: PDB / ID: 9n51
TitleCrosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and Crosslinker-crypto Human Mitochondrial Acyl Carrier Protein, C8Cl-mACP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
  • Acyl carrier protein, mitochondrial
KeywordsBIOSYNTHETIC PROTEIN / Crosslinked Complex / Human mitochondria / Type II Fatty Acid Biosynthesis / Ketosynthase
Function / homology
Function and homology information


short-chain fatty acid biosynthetic process / medium-chain fatty acid biosynthetic process / acyl-CoA metabolic process / protein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / beta-ketoacyl-[acyl-carrier-protein] synthase I / mitochondrial [2Fe-2S] assembly complex ...short-chain fatty acid biosynthetic process / medium-chain fatty acid biosynthetic process / acyl-CoA metabolic process / protein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / beta-ketoacyl-[acyl-carrier-protein] synthase I / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Mitochondrial protein degradation / aerobic respiration / fatty acid binding / mitochondrial membrane / fatty acid biosynthetic process / mitochondrial inner membrane / mitochondrial matrix / calcium ion binding / structural molecule activity / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
: / Acyl carrier protein, mitochondrial / 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSuo, Y. / Jiang, Z. / Heberlig, G.W. / Wang, E.Y. / Chen, A. / Sankaran, B. / La Clair, J.J. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG073807 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Role of Human Mitochondrial Ketosynthase in Long-Chain Fatty Acid Biosynthesis.
Authors: Suo, Y. / Jiang, Z. / Heberlig, G.W. / Wang, E.Y. / Sankaran, B. / La Clair, J.J. / Burkart, M.D.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 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: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
B: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
C: Acyl carrier protein, mitochondrial
D: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
E: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
F: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,9088
Polymers199,9736
Non-polymers9352
Water2,414134
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
B: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
C: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4544
Polymers99,9863
Non-polymers4671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-49 kcal/mol
Surface area30150 Å2
MethodPISA
2
D: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
E: 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
F: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4544
Polymers99,9863
Non-polymers4671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-50 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 118.630, 132.510
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial / Beta-ketoacyl-ACP synthase


Mass: 44903.906 Da / Num. of mol.: 4 / Fragment: residues 38-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OXSM / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NWU1, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 10178.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDUFAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14561
#3: Chemical ChemComp-A1BMZ / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethyl)-beta-alaninamide


Mass: 467.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H38N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M ammonium sulfate, 1 M lithium sulfate, and 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.31→53.64 Å / Num. obs: 104006 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.979 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.151 / Rrim(I) all: 0.322 / Χ2: 0.84 / Net I/σ(I): 4.4
Reflection shellResolution: 2.31→2.35 Å / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 3.257 / Num. measured all: 22413 / Num. unique obs: 5146 / CC1/2: 0.263 / Rpim(I) all: 1.721 / Rrim(I) all: 3.695 / Χ2: 0.85 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→53.64 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.273 --
Rwork0.245 --
obs-103944 99.9 %
Refinement stepCycle: LAST / Resolution: 2.31→53.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13808 0 60 134 14002

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