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- PDB-6cfo: HUMAN PYRUVATE DEHYDROGENASE E1 COMPONENT COMPLEX WITH COVALENT T... -

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Basic information

Entry
Database: PDB / ID: 6cfo
TitleHUMAN PYRUVATE DEHYDROGENASE E1 COMPONENT COMPLEX WITH COVALENT TDP ADDUCT ACETYL PHOSPHINATE
Components
  • Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
  • Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
KeywordsOXIDOREDUCTASE / THIAMIN PYROPHOSPHATE / ACETYL PHOSPHINATE / INHIBITOR / PYRUVATE DEHYDROGENASE
Function / homology
Function and homology information


: / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / PDH complex synthesizes acetyl-CoA from PYR / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / Mitochondrial protein degradation ...: / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / PDH complex synthesizes acetyl-CoA from PYR / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / Mitochondrial protein degradation / glucose metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A5X / Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsARJUNAN, P. / WHITLEY, M.J. / FUREY, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK080748 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the alpha V138M variant of human pyruvate dehydrogenase.
Authors: Whitley, M.J. / Arjunan, P. / Nemeria, N.S. / Korotchkina, L.G. / Park, Y.H. / Patel, M.S. / Jordan, F. / Furey, W.
History
DepositionFeb 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 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.title / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
B: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
C: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
D: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2388
Polymers156,1234
Non-polymers1,1154
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: known in literature
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20230 Å2
ΔGint-133 kcal/mol
Surface area41870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.270, 120.730, 129.780
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 Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / PDHE1-A type I


Mass: 40714.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHA1, PHE1A / Plasmid: PQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein Pyruvate dehydrogenase E1 component subunit beta, mitochondrial / PDHE1-B


Mass: 37346.836 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHB, PHE1B / Plasmid: PQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring)
#3: Chemical ChemComp-A5X / 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium


Mass: 533.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N4O10P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350, SODIUM THIOCYANATE, MAGNESIUM CHLORIDE, THIAMIN PYROPHOSPHATE, ACETYL PHOSPHINATE,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47.575 Å / Num. obs: 44058 / % possible obs: 98.33 % / Observed criterion σ(I): 0 / Redundancy: 6.966 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.89
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.28 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NI4

1ni4


Resolution: 2.7→47.575 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 2205 5 %
Rwork0.1856 --
obs0.1881 44058 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10698 0 66 375 11139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510988
X-RAY DIFFRACTIONf_angle_d0.92214860
X-RAY DIFFRACTIONf_dihedral_angle_d13.3714142
X-RAY DIFFRACTIONf_chiral_restr0.0611602
X-RAY DIFFRACTIONf_plane_restr0.0041944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75870.3211430.2542600X-RAY DIFFRACTION99
2.7587-2.82280.33481580.24372579X-RAY DIFFRACTION100
2.8228-2.89340.31791510.24912597X-RAY DIFFRACTION99
2.8934-2.97160.31981320.23792606X-RAY DIFFRACTION99
2.9716-3.05910.31691460.23192616X-RAY DIFFRACTION100
3.0591-3.15780.26691400.23042588X-RAY DIFFRACTION99
3.1578-3.27060.28161160.22812620X-RAY DIFFRACTION99
3.2706-3.40150.27781190.2312626X-RAY DIFFRACTION98
3.4015-3.55630.31141530.2322567X-RAY DIFFRACTION98
3.5563-3.74370.34121300.26542543X-RAY DIFFRACTION96
3.7437-3.97820.25121220.21062565X-RAY DIFFRACTION96
3.9782-4.28510.20931330.15182569X-RAY DIFFRACTION96
4.2851-4.7160.15811370.12652567X-RAY DIFFRACTION97
4.716-5.39760.16911300.12712676X-RAY DIFFRACTION98
5.3976-6.79730.18341520.1492712X-RAY DIFFRACTION100
6.7973-47.58260.18511430.15782822X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.637-0.08480.14760.68090.19181.22420.00390.1541-0.0701-0.1072-0.02330.0245-0.0481-0.01160.01510.3520.0028-0.00370.399-0.02370.3732-0.3223-8.1953-69.6001
21.21550.10730.22380.92750.371.80060.00480.0845-0.060.0986-0.0149-0.01940.06610.18190.01080.34140.01740.01740.28340.02240.38286.4445-8.3684-35.7531
31.150.2193-0.3291.6523-0.33511.53110.0312-0.1957-0.05550.35280.00160.1337-0.11490.023-0.02320.39050.00430.02320.35130.01020.3182-11.06070.7084-19.2297
41.45670.3102-0.18010.6391-0.00110.7828-0.0236-0.08220.00680.0749-0.0052-0.1407-0.06310.20220.0290.4763-0.0219-0.01830.38790.04920.442922.021621.7811-40.5021
51.50060.49820.2061.04510.16321.1574-0.05540.1490.122-0.01360.0093-0.0065-0.1151-0.00070.0480.3682-0.00590.01290.29460.02630.3378-10.292519.4334-52.219
60.8037-0.1739-0.50760.94880.1120.80950.04820.0751-0.03250.1146-0.03360.1880.0094-0.2167-0.00340.3889-0.00480.02390.45030.03750.46-28.11837.1738-38.2596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 361)
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 194)
3X-RAY DIFFRACTION3chain 'B' and (resid 195 through 329)
4X-RAY DIFFRACTION4chain 'C' and (resid 0 through 361)
5X-RAY DIFFRACTION5chain 'D' and (resid 0 through 194)
6X-RAY DIFFRACTION6chain 'D' and (resid 195 through 329)

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