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- PDB-5zqz: Structure of human mitochondrial trifunctional protein, tetramer -

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Basic information

Entry
Database: PDB / ID: 5zqz
TitleStructure of human mitochondrial trifunctional protein, tetramer
Components
  • Trifunctional enzyme subunit alpha, mitochondrial
  • Trifunctional enzyme subunit beta, mitochondrial
KeywordsLYASE / HYDROLASE/TRANSFERASE / fatty acid beta-oxidation / cryo-EM single-particle reconstruction / mitochondrial trifunctional protein / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase / Beta oxidation of myristoyl-CoA to lauroyl-CoA / cardiolipin acyl-chain remodeling / Acyl chain remodeling of CL / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / mitochondrial fatty acid beta-oxidation multienzyme complex / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / 3-hydroxyacyl-CoA dehydratase activity ...long-chain-3-hydroxyacyl-CoA dehydrogenase / Beta oxidation of myristoyl-CoA to lauroyl-CoA / cardiolipin acyl-chain remodeling / Acyl chain remodeling of CL / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / mitochondrial fatty acid beta-oxidation multienzyme complex / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / 3-hydroxyacyl-CoA dehydratase activity / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase / acetyl-CoA C-acetyltransferase activity / 3-hydroxyacyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / enoyl-CoA hydratase activity / mitochondrial envelope / lncRNA binding / fatty acid beta-oxidation / mitochondrial nucleoid / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to insulin / gene expression / mitochondrial inner membrane / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to xenobiotic stimulus / protein-containing complex binding / endoplasmic reticulum / mitochondrion / RNA binding
Similarity search - Function
Fatty acid oxidation complex, alpha subunit, mitochondrial / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site ...Fatty acid oxidation complex, alpha subunit, mitochondrial / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Trifunctional enzyme subunit alpha, mitochondrial / Trifunctional enzyme subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLiang, K. / Li, N. / Dai, J. / Wang, X. / Liu, P. / Chen, X. / Wang, C. / Gao, N. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Cryo-EM structure of human mitochondrial trifunctional protein.
Authors: Kai Liang / Ningning Li / Xiao Wang / Jianye Dai / Pulan Liu / Chu Wang / Xiao-Wei Chen / Ning Gao / Junyu Xiao /
Abstract: The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid β-oxidation process. Mutations in the two TFP subunits cause mitochondrial trifunctional protein deficiency ...The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid β-oxidation process. Mutations in the two TFP subunits cause mitochondrial trifunctional protein deficiency and acute fatty liver of pregnancy that can lead to death. Here we report a 4.2-Å cryo-electron microscopy α2β2 tetrameric structure of the human TFP. The tetramer has a V-shaped architecture that displays a distinct assembly compared with the bacterial TFPs. A concave surface of the TFP tetramer interacts with the detergent molecules in the structure, suggesting that this region is involved in associating with the membrane. Deletion of a helical hairpin in TFPβ decreases its binding to the liposomes in vitro and reduces its membrane targeting in cells. Our results provide the structural basis for TFP function and have important implications for fatty acid oxidation related diseases.
History
DepositionApr 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Trifunctional enzyme subunit alpha, mitochondrial
B: Trifunctional enzyme subunit beta, mitochondrial
C: Trifunctional enzyme subunit alpha, mitochondrial
D: Trifunctional enzyme subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)268,9464
Polymers268,9464
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11560 Å2
ΔGint-56 kcal/mol
Surface area101950 Å2

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Components

#1: Protein Trifunctional enzyme subunit alpha, mitochondrial / 78 kDa gastrin-binding protein / TP-alpha


Mass: 83112.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADHA, HADH / Production host: Escherichia coli (E. coli)
References: UniProt: P40939, enoyl-CoA hydratase, long-chain-3-hydroxyacyl-CoA dehydrogenase
#2: Protein Trifunctional enzyme subunit beta, mitochondrial / TP-beta


Mass: 51360.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADHB, MSTP029 / Production host: Escherichia coli (E. coli) / References: UniProt: P55084, acetyl-CoA C-acyltransferase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human mitochondrial trifunctional protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 426969 / Details: Gold Standard / Symmetry type: POINT

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