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- PDB-2f5z: Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Co... -

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Basic information

Entry
Database: PDB / ID: 2f5z
TitleCrystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein
Components
  • Dihydrolipoyl dehydrogenase
  • Pyruvate dehydrogenase protein X component
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / protein-protein complex / OXIDOREDUCTASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD ...acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / PDH complex synthesizes acetyl-CoA from PYR / Branched-chain ketoacid dehydrogenase kinase deficiency / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / Regulation of pyruvate dehydrogenase (PDH) complex / oxoglutarate dehydrogenase complex / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / 2-oxoglutarate metabolic process / pyruvate metabolic process / Signaling by Retinoic Acid / motile cilium / acyltransferase activity / sperm capacitation / mitochondrial electron transport, NADH to ubiquinone / gastrulation / Mitochondrial protein degradation / regulation of membrane potential / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Dihydrolipoamide dehydrogenase / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site ...E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Dihydrolipoamide dehydrogenase / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme / FAD/NAD-linked reductase, dimerisation domain superfamily / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Pyruvate dehydrogenase protein X component, mitochondrial / Dihydrolipoyl dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBrautigam, C.A. / Chuang, J.L. / Wynn, R.M. / Tomchick, D.R. / Machius, M. / Chuang, D.T.
CitationJournal: Structure / Year: 2006
Title: Structural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex.
Authors: Brautigam, C.A. / Wynn, R.M. / Chuang, J.L. / Machius, M. / Tomchick, D.R. / Chuang, D.T.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS ...BIOMOLECULE: 1, 2, 3, 4, 5 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 15CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS INDICATE THAT BIOMOLECULE 1 BEST REPRESENTS THE PHYSIOLOGICAL COMPLEX

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
E: Dihydrolipoyl dehydrogenase
F: Dihydrolipoyl dehydrogenase
G: Dihydrolipoyl dehydrogenase
H: Dihydrolipoyl dehydrogenase
I: Dihydrolipoyl dehydrogenase
J: Dihydrolipoyl dehydrogenase
K: Pyruvate dehydrogenase protein X component
L: Pyruvate dehydrogenase protein X component
M: Pyruvate dehydrogenase protein X component
N: Pyruvate dehydrogenase protein X component
O: Pyruvate dehydrogenase protein X component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)549,43764
Polymers537,83515
Non-polymers11,60249
Water31,9951776
1
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
K: Pyruvate dehydrogenase protein X component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,90713
Polymers107,5673
Non-polymers2,34010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
L: Pyruvate dehydrogenase protein X component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,90713
Polymers107,5673
Non-polymers2,34010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Dihydrolipoyl dehydrogenase
F: Dihydrolipoyl dehydrogenase
M: Pyruvate dehydrogenase protein X component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,90713
Polymers107,5673
Non-polymers2,34010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Dihydrolipoyl dehydrogenase
H: Dihydrolipoyl dehydrogenase
N: Pyruvate dehydrogenase protein X component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,90713
Polymers107,5673
Non-polymers2,34010
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Dihydrolipoyl dehydrogenase
J: Dihydrolipoyl dehydrogenase
O: Pyruvate dehydrogenase protein X component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,81112
Polymers107,5673
Non-polymers2,2449
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.153, 187.728, 224.392
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
Dihydrolipoyl dehydrogenase / Dihydrolipoamide dehydrogenase / Glycine cleavage system L protein


Mass: 50208.406 Da / Num. of mol.: 10 / Fragment: Dihydrolipoyl dehydrogenase, residues 36-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: pTrcHisThE3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: P09622, dihydrolipoyl dehydrogenase
#2: Protein
Pyruvate dehydrogenase protein X component / Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / Lipoyl- ...Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / Lipoyl-containing pyruvate dehydrogenase complex component X / E3-binding protein / E3BP / proX


Mass: 7150.151 Da / Num. of mol.: 5 / Fragment: E3-binding domain, residues 173-230 / Mutation: K120G,T176L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHX, PDX1 / Plasmid: pET-LTE3BD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: O00330
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1776 / Source method: isolated from a natural source / Formula: H2O
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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 14% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, 0.03 M spermidine, 8% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979426 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 9, 2004
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979426 Å / Relative weight: 1
ReflectionResolution: 2.18→37.4 Å / Num. all: 367237 / Num. obs: 367237 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.054 / Net I/σ(I): 21.9
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 31492 / Rsym value: 0.401 / % possible all: 84.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZMD without NADH

1zmd


Resolution: 2.18→37.4 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues of E3BD with missing atoms were modeled as alanine due to missing density for the side chain
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4518 -random
Rwork0.205 ---
all0.205 367237 --
obs0.205 367068 98.1 %-
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.68 Å20 Å20 Å2
2---0.94 Å20 Å2
3---6.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.18→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37675 0 725 1776 40176
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_deg2.02
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.33 749 -
Rwork0.288 --
obs-55131 90.4 %

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