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Basic information

Entry
Database: PDB / ID: 3exf
TitleCrystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex
Components(Pyruvate dehydrogenase E1 component subunit ...) x 2
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 / SYNCHROTRON / Resolution: 2.998 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 / 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 / _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 / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
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)315,93020
Polymers313,9758
Non-polymers1,95512
Water1629
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)157,96510
Polymers156,9884
Non-polymers9776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22070 Å2
ΔGint-155 kcal/mol
Surface area41930 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)157,96510
Polymers156,9884
Non-polymers9776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22100 Å2
ΔGint-150 kcal/mol
Surface area42190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.389, 129.668, 144.946
Angle α, β, γ (deg.)90.000, 109.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERAA0 - 36121 - 382
21METMETSERSERCC0 - 36121 - 382
31METMETSERSEREE0 - 36121 - 382
41METMETSERSERGG0 - 36121 - 382
12LEULEUILEILEBB1 - 3291 - 329
22LEULEUILEILEDD1 - 3291 - 329
32LEULEUILEILEFF1 - 3291 - 329
42LEULEUILEILEHH1 - 3291 - 329

NCS ensembles :
ID
1
2

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Components

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Pyruvate dehydrogenase E1 component subunit ... , 2 types, 8 molecules ACEGBDFH

#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.: 4 / Fragment: E1p-alpha / Mutation: S203A,S271A
Source method: isolated from a genetically manipulated source
Details: Phosphorylation site 1 (S264) only mutant (S203A/S271A) with bound Mg-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)
#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 , 4 types, 21 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.998→50 Å / Num. obs: 72201 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.146 / Χ2: 1.448 / Net I/σ(I): 10.699
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.998-3.053.40.5635431.568198.2
3.05-3.113.70.52435761.651100
3.11-3.173.70.43536371.4111100
3.17-3.233.70.36736231.373199.9
3.23-3.33.70.31235701.3431100
3.3-3.383.70.27235831.4071100
3.38-3.463.80.23936031.432199.9
3.46-3.563.80.19235961.4191100
3.56-3.663.80.17336031.5361100
3.66-3.783.80.15436081.581199.8
3.78-3.913.80.14436171.573199.9
3.91-4.073.80.12235821.533199.9
4.07-4.263.80.11136311.669199.8
4.26-4.483.70.09336071.592199.5
4.48-4.763.80.08235711.517199.6
4.76-5.133.70.08236371.404199.9
5.13-5.643.70.08336051.32199.8
5.64-6.463.90.0836491.283199.9
6.46-8.133.90.06336491.218199.9
8.13-503.70.05137111.162199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementResolution: 2.998→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.839 / Occupancy max: 1 / Occupancy min: 1 / SU B: 38.314 / SU ML: 0.324 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3624 5 %RANDOM
Rwork0.185 ---
obs0.189 72121 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.88 Å2 / Biso mean: 21.411 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å21.8 Å2
2---3.18 Å20 Å2
3---4.28 Å2
Refinement stepCycle: LAST / Resolution: 2.998→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21386 0 112 9 21507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02221940
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.96829664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30752758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91923.967978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.975153744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.64915148
X-RAY DIFFRACTIONr_chiral_restr0.1220.23194
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116744
X-RAY DIFFRACTIONr_mcbond_it0.6641.513714
X-RAY DIFFRACTIONr_mcangle_it1.342221998
X-RAY DIFFRACTIONr_scbond_it2.28738226
X-RAY DIFFRACTIONr_scangle_it3.8834.57666
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1444MEDIUM POSITIONAL0.230.5
1B1444MEDIUM POSITIONAL0.240.5
1C1444MEDIUM POSITIONAL0.220.5
1D1444MEDIUM POSITIONAL0.240.5
1A1372LOOSE POSITIONAL0.565
1B1372LOOSE POSITIONAL0.585
1C1372LOOSE POSITIONAL0.575
1D1372LOOSE POSITIONAL0.625
1A1444MEDIUM THERMAL1.92
1B1444MEDIUM THERMAL1.712
1C1444MEDIUM THERMAL2.142
1D1444MEDIUM THERMAL1.972
1A1372LOOSE THERMAL2.9510
1B1372LOOSE THERMAL2.7110
1C1372LOOSE THERMAL3.2110
1D1372LOOSE THERMAL2.810
2E1316MEDIUM POSITIONAL0.20.5
2F1316MEDIUM POSITIONAL0.20.5
2G1316MEDIUM POSITIONAL0.20.5
2H1316MEDIUM POSITIONAL0.210.5
2E1203LOOSE POSITIONAL0.55
2F1203LOOSE POSITIONAL0.495
2G1203LOOSE POSITIONAL0.535
2H1203LOOSE POSITIONAL0.515
2E1316MEDIUM THERMAL1.72
2F1316MEDIUM THERMAL1.722
2G1316MEDIUM THERMAL1.782
2H1316MEDIUM THERMAL1.852
2E1203LOOSE THERMAL2.5410
2F1203LOOSE THERMAL2.6810
2G1203LOOSE THERMAL2.5510
2H1203LOOSE THERMAL2.7810
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 235 -
Rwork0.24 4815 -
all-5050 -
obs--94.09 %
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)
10.4561-0.0974-0.01390.4239-0.02940.30650.0119-0.0053-0.01390.0155-0.0023-0.0513-0.04640.0399-0.0097-0.0659-0.0186-0.0044-0.0606-0.0405-0.0826-25.084-8.173-6.732
20.40610.11310.02570.4028-0.07890.31850.02480.0220.0275-0.0101-0.0002-0.01190.02680.0257-0.0246-0.04930.00860.0066-0.0558-0.0368-0.082-52.927-42.089-61.709
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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