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- EMDB-6940: Structure of human mitochondrial trifunctional protein, tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-6940
TitleStructure of human mitochondrial trifunctional protein, tetramer
Map data
Sample
  • Complex: human mitochondrial trifunctional protein
    • Protein or peptide: Trifunctional enzyme subunit alpha, mitochondrial
    • Protein or peptide: Trifunctional enzyme subunit beta, mitochondrial
Keywordsfatty acid beta-oxidation / cryo-EM single-particle reconstruction / mitochondrial trifunctional protein / LYASE / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase / Acyl chain remodeling of CL / Beta oxidation of myristoyl-CoA to lauroyl-CoA / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / cardiolipin acyl-chain remodeling / 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 / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA ...long-chain-3-hydroxyacyl-CoA dehydrogenase / Acyl chain remodeling of CL / Beta oxidation of myristoyl-CoA to lauroyl-CoA / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / cardiolipin acyl-chain remodeling / 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 / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydratase activity / 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 / cellular response to lipopolysaccharide / mitochondrial outer membrane / mitochondrial inner 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. ...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. / Thiolase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Thiolase, C-terminal domain / Enoyl-CoA hydratase/isomerase signature. / Thiolase / 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)
Methodsingle 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
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, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseJun 20, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-5zqz
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6940.png

Downloads & links

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Map

FileDownload / File: emd_6940.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 180 pix.
= 237.6 Å		1.32 Å/pix.
x 180 pix.
= 237.6 Å		1.32 Å/pix.
x 180 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.17336836 - 0.34049574
Average (Standard dev.)0.00078695384 (±0.008788166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z237.600237.600237.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1730.3400.001

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Supplemental data

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Sample components

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Entire : human mitochondrial trifunctional protein

EntireName: human mitochondrial trifunctional protein
Components
  • Complex: human mitochondrial trifunctional protein
    • Protein or peptide: Trifunctional enzyme subunit alpha, mitochondrial
    • Protein or peptide: Trifunctional enzyme subunit beta, mitochondrial

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Supramolecule #1: human mitochondrial trifunctional protein

SupramoleculeName: human mitochondrial trifunctional protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Trifunctional enzyme subunit alpha, mitochondrial

MacromoleculeName: Trifunctional enzyme subunit alpha, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: enoyl-CoA hydratase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.112625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVACRAIGIL SRFSAFRILR SRGYICRNFT GSSALLTRTH INYGVKGDVA VVRINSPNSK VNTLSKELHS EFSEVMNEIW ASDQIRSAV LISSKPGCFI AGADINMLAA CKTLQEVTQL SQEAQRIVEK LEKSTKPIVA AINGSCLGGG LEVAISCQYR I ATKDRKTV ...String:
MVACRAIGIL SRFSAFRILR SRGYICRNFT GSSALLTRTH INYGVKGDVA VVRINSPNSK VNTLSKELHS EFSEVMNEIW ASDQIRSAV LISSKPGCFI AGADINMLAA CKTLQEVTQL SQEAQRIVEK LEKSTKPIVA AINGSCLGGG LEVAISCQYR I ATKDRKTV LGTPEVLLGA LPGAGGTQRL PKMVGVPAAL DMMLTGRSIR ADRAKKMGLV DQLVEPLGPG LKPPEERTIE YL EEVAITF AKGLADKKIS PKRDKGLVEK LTAYAMTIPF VRQQVYKKVE EKVRKQTKGL YPAPLKIIDV VKTGIEQGSD AGY LCESQK FGELVMTKES KALMGLYHGQ VLCKKNKFGA PQKDVKHLAI LGAGLMGAGI AQVSVDKGLK TILKDATLTA LDRG QQQVF KGLNDKVKKK ALTSFERDSI FSNLTGQLDY QGFEKADMVI EAVFEDLSLK HRVLKEVEAV IPDHCIFASN TSALP ISEI AAVSKRPEKV IGMHYFSPVD KMQLLEIITT EKTSKDTSAS AVAVGLKQGK VIIVVKDGPG FYTTRCLAPM MSEVIR ILQ EGVDPKKLDS LTTSFGFPVG AATLVDEVGV DVAKHVAEDL GKVFGERFGG GNPELLTQMV SKGFLGRKSG KGFYIYQ EG VKRKDLNSDM DSILASLKLP PKSEVSSDED IQFRLVTRFV NEAVMCLQEG ILATPAEGDI GAVFGLGFPP CLGGPFRF V DLYGAQKIVD RLKKYEAAYG KQFTPCQLLA DHANSPNKKF YQ

UniProtKB: Trifunctional enzyme subunit alpha, mitochondrial

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Macromolecule #2: Trifunctional enzyme subunit beta, mitochondrial

MacromoleculeName: Trifunctional enzyme subunit beta, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetyl-CoA C-acyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.360359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTILTYPFKN LPTASKWALR FSIRPLSCSS QLRAAPAVQT KTKKTLAKPN IRNVVVVDGV RTPFLLSGTS YKDLMPHDLA RAALTGLLH RTSVPKEVVD YIIFGTVIQE VKTSNVAREA ALGAGFSDKT PAHTVTMACI SANQAMTTGV GLIASGQCDV I VAGGVELM ...String:
MTILTYPFKN LPTASKWALR FSIRPLSCSS QLRAAPAVQT KTKKTLAKPN IRNVVVVDGV RTPFLLSGTS YKDLMPHDLA RAALTGLLH RTSVPKEVVD YIIFGTVIQE VKTSNVAREA ALGAGFSDKT PAHTVTMACI SANQAMTTGV GLIASGQCDV I VAGGVELM SDVPIRHSRK MRKLMLDLNK AKSMGQRLSL ISKFRFNFLA PELPAVSEFS TSETMGHSAD RLAAAFAVSR LE QDEYALR SHSLAKKAQD EGLLSDVVPF KVPGKDTVTK DNGIRPSSLE QMAKLKPAFI KPYGTVTAAN SSFLTDGASA MLI MAEEKA LAMGYKPKAY LRDFMYVSQD PKDQLLLGPT YATPKVLEKA GLTMNDIDAF EFHEAFSGQI LANFKAMDSD WFAE NYMGR KTKVGLPPLE KFNNWGGSLS LGHPFGATGC RLVMAAANRL RKEGGQYGLV AACAAGGQGH AMIVEAYPK

UniProtKB: Trifunctional enzyme subunit beta, mitochondrial

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Gold Standard / Number images used: 426969
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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