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Basic information

Entry
Database: PDB / ID: 3exh
TitleCrystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex
Components
  • (Pyruvate dehydrogenase E1 component subunit alpha, somatic form, ...) x 2
  • Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
KeywordsOXIDOREDUCTASE / heterotetramer / thiamine diphosphate-dependent enzyme / Disease mutation / Glycolysis / Leigh syndrome / Mitochondrion / Phosphoprotein / Alternative splicing / Polymorphism / Pyruvate / Thiamine pyrophosphate / Transit peptide
Function / homology
Function and homology information


pyruvate dehydrogenase (NAD+) activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid ...pyruvate dehydrogenase (NAD+) activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain ...Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / 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
: / : / THIAMINE DIPHOSPHATE / 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 / Resolution: 2.444 Å
AuthorsKato, M. / Wynn, R.M. / Chuang, J.L. / Tso, S.-C. / Machius, M. / Li, J. / Chuang, D.T.
CitationJournal: Structure / Year: 2008
Title: Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
Authors: Kato, M. / Wynn, R.M. / Chuang, J.L. / Tso, S.C. / Machius, M. / Li, J. / Chuang, D.T.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
E: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
F: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
G: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
H: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,67325
Polymers314,1358
Non-polymers2,53817
Water14,268792
1
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)158,38313
Polymers157,0684
Non-polymers1,3159
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23490 Å2
ΔGint-153 kcal/mol
Surface area41890 Å2
MethodPISA
2
E: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
F: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
G: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
H: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,29112
Polymers157,0684
Non-polymers1,2238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22050 Å2
ΔGint-146 kcal/mol
Surface area41320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)257.064, 115.612, 127.592
Angle α, β, γ (deg.)90.000, 113.640, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA1 - 3291 - 329
211CC1 - 3291 - 329
311EE1 - 3291 - 329
411GG1 - 3291 - 329
112BB0 - 1970 - 197
212DD0 - 1970 - 197
312FF0 - 1970 - 197
412HH0 - 1970 - 197
122BB205 - 258205 - 258
222DD205 - 258205 - 258
322FF205 - 258205 - 258
422HH205 - 258205 - 258
132BB283 - 361283 - 361
232DD283 - 361283 - 361
332FF283 - 361283 - 361
432HH283 - 361283 - 361

NCS ensembles :
ID
1
2

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Components

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Pyruvate dehydrogenase E1 component subunit alpha, somatic form, ... , 2 types, 4 molecules AECG

#1: Protein Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / E.C.1.2.4.1 / pyruvate dehydrogenase (E1p) alpha subunit / PDHE1-A type I


Mass: 42552.516 Da / Num. of mol.: 2 / Fragment: E1p-alpha / Mutation: S203A,S271A
Source method: isolated from a genetically manipulated source
Details: S203A/S271A with bound Mn-ThDP / Source: (gene. exp.) Homo sapiens (human) / Gene: PDHA1, PHE1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)
#3: Protein Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / E.C.1.2.4.1 / pyruvate dehydrogenase (E1p) alpha subunit / PDHE1-A type I


Mass: 42632.492 Da / Num. of mol.: 2 / Fragment: E1p-alpha / Mutation: S203A,S271A
Source method: isolated from a genetically manipulated source
Details: phosphorylated S264, S203A/S271A with bound Mn-ThDP
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHA1, PHE1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)

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Protein , 1 types, 4 molecules BDFH

#2: Protein
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial / E.C.1.2.4.1 / pyruvate dehydrogenase (E1p) beta subunit / PDHE1-B


Mass: 35941.316 Da / Num. of mol.: 4 / Fragment: E1p-beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHB, PHE1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring)

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Non-polymers , 5 types, 809 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 8000, 140mM NaOAC, 50mM BisTris pH6.5, 10% glucose, 50mM Taurine, 8mM MgCl2, and 10mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.444→50 Å / Num. obs: 123888 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.155 / Χ2: 1.296 / Net I/σ(I): 14.158
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.444-2.496.50.69360361.081196.6
2.49-2.546.80.65960971.094197
2.54-2.596.90.58560791.093197.1
2.59-2.646.80.51561101.118197.3
2.64-2.76.90.44161521.165197.3
2.7-2.766.80.39761401.14197.5
2.76-2.836.80.36161311.189197.6
2.83-2.96.80.33561641.183197.8
2.9-2.996.80.27561201.231197.9
2.99-3.096.80.23361761.268198.1
3.09-3.26.80.20862141.295198.2
3.2-3.326.80.17662091.382198.4
3.32-3.486.80.16961991.56198.5
3.48-3.666.70.1562331.765198.6
3.66-3.896.70.12362331.685198.7
3.89-4.196.70.162391.597198.9
4.19-4.616.70.07962791.451199.1
4.61-5.286.70.07263241.287199.4
5.28-6.656.70.07763401.238199.6
6.65-506.20.0564131.083199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementResolution: 2.444→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.465 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 6182 5 %RANDOM
Rwork0.165 ---
obs0.167 123754 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.61 Å2 / Biso mean: 18.89 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0.25 Å2
2--0.62 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.444→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21101 0 142 792 22035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02221669
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9729289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18752719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80824.035964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59215.0083695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.68715144
X-RAY DIFFRACTIONr_chiral_restr0.1150.23154
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02116496
X-RAY DIFFRACTIONr_mcbond_it0.8061.513534
X-RAY DIFFRACTIONr_mcangle_it1.548221703
X-RAY DIFFRACTIONr_scbond_it2.91738135
X-RAY DIFFRACTIONr_scangle_it4.6374.57586
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1192MEDIUM POSITIONAL0.20.5
1B1192MEDIUM POSITIONAL0.210.5
1C1192MEDIUM POSITIONAL0.360.5
1D1192MEDIUM POSITIONAL0.210.5
1A1113LOOSE POSITIONAL0.575
1B1113LOOSE POSITIONAL0.565
1C1113LOOSE POSITIONAL0.825
1D1113LOOSE POSITIONAL0.535
1A1192MEDIUM THERMAL1.232
1B1192MEDIUM THERMAL1.182
1C1192MEDIUM THERMAL1.592
1D1192MEDIUM THERMAL1.452
1A1113LOOSE THERMAL1.810
1B1113LOOSE THERMAL1.7210
1C1113LOOSE THERMAL2.0710
1D1113LOOSE THERMAL2.0710
2E1192MEDIUM POSITIONAL0.10.5
2F1192MEDIUM POSITIONAL0.10.5
2G1192MEDIUM POSITIONAL0.110.5
2H1192MEDIUM POSITIONAL0.110.5
2E1097LOOSE POSITIONAL0.385
2F1097LOOSE POSITIONAL0.395
2G1097LOOSE POSITIONAL0.415
2H1097LOOSE POSITIONAL0.415
2E1192MEDIUM THERMAL1.352
2F1192MEDIUM THERMAL1.142
2G1192MEDIUM THERMAL1.412
2H1192MEDIUM THERMAL1.622
2E1097LOOSE THERMAL2.210
2F1097LOOSE THERMAL2.1410
2G1097LOOSE THERMAL2.3910
2H1097LOOSE THERMAL2.5510
LS refinement shellResolution: 2.444→2.507 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 416 -
Rwork0.234 8258 -
all-8674 -
obs--93.05 %
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)
10.5852-0.0049-0.07560.39070.06070.65670.0031-0.0036-0.00170.02050.0336-0.03630.05730.1224-0.0368-0.08620.0123-0.0092-0.0946-0.0003-0.0927-41.8856.8428.26
20.5026-0.0276-0.09520.3922-0.02750.86770.0267-0.07380.04270.01950.0086-0.0183-0.01480.0972-0.0352-0.109-0.00670.0022-0.1033-0.0042-0.0807-18.21386.116-47.733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 361
2X-RAY DIFFRACTION1B1 - 329
3X-RAY DIFFRACTION1C0 - 361
4X-RAY DIFFRACTION1D1 - 329
5X-RAY DIFFRACTION2E0 - 361
6X-RAY DIFFRACTION2F1 - 329
7X-RAY DIFFRACTION2G0 - 361
8X-RAY DIFFRACTION2H1 - 329

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