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- PDB-2a1t: Structure of the human MCAD:ETF E165betaA complex -

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Basic information

Entry
Database: PDB / ID: 2a1t
TitleStructure of the human MCAD:ETF E165betaA complex
Components
  • (Electron transfer flavoprotein ...) x 2
  • Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / electron transfer / domain dynamics / conformational sampling / protein:protein complex / fatty acid b-degradation / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
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 / response to starvation / fatty acid beta-oxidation / Protein methylation / response to cold / post-embryonic development / respiratory electron transport chain / liver development / PPARA activates gene expression / mitochondrial membrane / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer 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 / TPP-binding domain / 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: 2.8 Å
AuthorsToogood, H.S. / Van Thiel, A. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Stabilization of Non-productive Conformations Underpins Rapid Electron Transfer to Electron-transferring Flavoprotein
Authors: Toogood, H.S. / van Thiel, A. / Scrutton, N.S. / Leys, D.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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 precursor
B: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor
C: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor
D: Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor
R: Electron transfer flavoprotein alpha-subunit, mitochondrial precursor
S: Electron transfer flavoprotein beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,81712
Polymers249,5426
Non-polymers4,2756
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33860 Å2
ΔGint-215 kcal/mol
Surface area69440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.184, 100.659, 244.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEULYSLYSAA10 - 39535 - 420
2LEULEUASNASNBB10 - 39635 - 421
3GLYGLYASNASNCC9 - 39634 - 421
4LEULEUASNASNDD10 - 39635 - 421

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 46648.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTRC99C / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P11310, EC: 1.3.99.3

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Electron transfer flavoprotein ... , 2 types, 2 molecules RS

#2: Protein Electron transfer flavoprotein alpha-subunit, mitochondrial precursor / Alpha-ETF


Mass: 35121.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P13804
#3: Protein Electron transfer flavoprotein beta-subunit / Beta-ETF


Mass: 27827.611 Da / Num. of mol.: 1 / Mutation: E165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P38117

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Non-polymers , 3 types, 70 molecules

#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 5 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 5000MME, 50mM sodium thiocyanate, sodium cacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2005
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 171306 / Num. obs: 55260 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.4
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.2.0011refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T9G

1t9g


Resolution: 2.8→19.98 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.87 / SU B: 16.374 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 2798 5 %RANDOM
Rwork0.199 ---
all0.2025 52662 --
obs0.2025 52662 100 %-
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: 42.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15837 0 288 64 16189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02216426
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214991
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.98622292
X-RAY DIFFRACTIONr_angle_other_deg0.902334771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09452092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85724.721682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.697152707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7191589
X-RAY DIFFRACTIONr_chiral_restr0.0860.22502
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023157
X-RAY DIFFRACTIONr_nbd_refined0.2280.24166
X-RAY DIFFRACTIONr_nbd_other0.1930.216232
X-RAY DIFFRACTIONr_nbtor_refined0.1890.28090
X-RAY DIFFRACTIONr_nbtor_other0.0910.29473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0780.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.521.510635
X-RAY DIFFRACTIONr_mcbond_other0.0841.54326
X-RAY DIFFRACTIONr_mcangle_it0.898216569
X-RAY DIFFRACTIONr_scbond_it1.20136906
X-RAY DIFFRACTIONr_scangle_it2.0734.55723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5650 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.635
2Bloose positional0.65
3Cloose positional0.65
4Dloose positional0.625
1Aloose thermal1.7110
2Bloose thermal2.6610
3Cloose thermal210
4Dloose thermal1.6610
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 192 -
Rwork0.317 3594 -
obs--100 %

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