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- PDB-1t9g: Structure of the human MCAD:ETF complex -

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Basic information

Entry
Database: PDB / ID: 1t9g
TitleStructure of the human MCAD:ETF complex
Components
  • Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial
  • Electron transfer flavoprotein alpha-subunit, mitochondrial
  • Electron transfer flavoprotein beta-subunit
Keywordsoxidoreductase / electron transport / electron transfer / protein:protein complex / fatty acid oxidation / human electron transferring flavoprotein / human medium chain acyl coa dehydrogenase
Function / homology
Function and homology information


electron transfer flavoprotein complex / medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / carnitine biosynthetic process / medium-chain fatty acid metabolic process ...electron transfer flavoprotein complex / medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / carnitine biosynthetic process / medium-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / Respiratory electron transport / amino acid catabolic process / cardiac muscle cell differentiation / glycogen biosynthetic process / regulation of gluconeogenesis / fatty acid beta-oxidation / response to starvation / Protein methylation / response to cold / liver development / post-embryonic development / respiratory electron transport chain / mitochondrial membrane / PPARA activates gene expression / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / mitochondrial matrix / axon / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Medium-chain specific acyl-CoA dehydrogenase / Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein domain / Electron transfer flavoprotein alpha subunit/FixB ...Medium-chain specific acyl-CoA dehydrogenase / Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein domain / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain / Electron transfer flavoprotein domain / : / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / DHS-like NAD/FAD-binding domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Medium-chain specific acyl-CoA dehydrogenase, mitochondrial / Electron transfer flavoprotein subunit alpha, mitochondrial / Electron transfer flavoprotein subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsToogood, H.S. / van Thiel, A. / Basran, J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Extensive domain motion and electron transfer in the human electron transferring flavoprotein-medium chain Acyl-CoA dehydrogenase complex
Authors: Toogood, H.S. / van Thiel, A. / Basran, J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
History
DepositionMay 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial
B: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial
C: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial
D: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial
R: Electron transfer flavoprotein alpha-subunit, mitochondrial
S: Electron transfer flavoprotein beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,28011
Polymers237,7906
Non-polymers3,4895
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.333, 101.322, 244.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial / MCAD


Mass: 43695.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACADM / Production host: Escherichia coli (E. coli) / References: UniProt: P11310, EC: 1.3.99.3
#2: Protein Electron transfer flavoprotein alpha-subunit, mitochondrial / Alpha-ETF


Mass: 35121.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETFA / Production host: Escherichia coli (E. coli) / References: UniProt: P13804
#3: Protein Electron transfer flavoprotein beta-subunit / Beta-ETF


Mass: 27885.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETFB / Production host: Escherichia coli (E. coli) / References: UniProt: P38117
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-15% PEG 2000 MME, 0.2 M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 51756 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.118 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.387 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.828 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26344 2614 5 %RANDOM
Rwork0.19097 ---
obs0.1947 49177 100 %-
all-49177 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14763 0 235 0 14998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02215280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.011.96820738
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27351954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5324.648639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.089152499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.891585
X-RAY DIFFRACTIONr_chiral_restr0.1330.22322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211494
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.27525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2576
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8231.59930
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.445215449
X-RAY DIFFRACTIONr_scbond_it2.19636231
X-RAY DIFFRACTIONr_scangle_it3.6274.55289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.458 156
Rwork0.302 2979

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