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Basic information

Entry
Database: PDB / ID: 3exe
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 / Mitochondrial protein degradation / 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: 1.979 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 1.3Dec 27, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _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.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.value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)316,54924
Polymers314,1038
Non-polymers2,44616
Water41,7232316
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)158,27512
Polymers157,0524
Non-polymers1,2238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22880 Å2
ΔGint-146 kcal/mol
Surface area41360 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)158,27512
Polymers157,0524
Non-polymers1,2238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22890 Å2
ΔGint-145 kcal/mol
Surface area41260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.572, 129.617, 124.303
Angle α, β, γ (deg.)90.000, 92.480, 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: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHESERSERAA1 - 36122 - 382
21PHEPHESERSERCC1 - 36122 - 382
31PHEPHESERSEREE1 - 36122 - 382
41PHEPHESERSERGG1 - 36122 - 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: 42584.516 Da / Num. of mol.: 4 / Fragment: E1p-alpha
Source method: isolated from a genetically manipulated source
Details: wild type 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)
#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, 2332 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2316 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
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: Oct 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.979→50 Å / Num. obs: 225065 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.107 / Χ2: 0.875 / Net I/σ(I): 13.345
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.979-2.034.80.551111850.709199
2.03-2.074.90.544111310.747199
2.07-2.114.90.433111620.919199.3
2.11-2.1550.373112000.735199.3
2.15-2.250.333112070.762199.4
2.2-2.2550.328111810.8199.2
2.25-2.3150.314112021.108199.5
2.31-2.3750.234112400.745199.4
2.37-2.4450.204112380.77199.7
2.44-2.5250.177112510.739199.6
2.52-2.614.90.155112800.741199.7
2.61-2.714.90.131112220.772199.8
2.71-2.844.90.107113070.76199.8
2.84-2.994.90.098112790.825199.9
2.99-3.174.90.08112780.971199.9
3.17-3.424.90.067112941.081100
3.42-3.764.80.061113221.1111100
3.76-4.314.70.053113701.1911100
4.31-5.434.40.045113621.079199.9
5.43-5050.042113540.986198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementResolution: 1.979→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.045 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 11272 5 %RANDOM
Rwork0.158 ---
obs0.161 224962 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.47 Å2 / Biso mean: 18.562 Å2 / Biso min: 3.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.41 Å2
2---0.47 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.979→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21379 0 136 2316 23831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02221952
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.96929670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28952756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6923.971977
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.989153751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7315148
X-RAY DIFFRACTIONr_chiral_restr0.1250.23192
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116730
X-RAY DIFFRACTIONr_mcbond_it0.9261.513704
X-RAY DIFFRACTIONr_mcangle_it1.583221991
X-RAY DIFFRACTIONr_scbond_it3.07438248
X-RAY DIFFRACTIONr_scangle_it4.8014.57679
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2818LOOSE POSITIONAL0.365
1B2818LOOSE POSITIONAL0.395
1C2818LOOSE POSITIONAL0.355
1D2818LOOSE POSITIONAL0.345
1A2818LOOSE THERMAL1.9810
1B2818LOOSE THERMAL1.9210
1C2818LOOSE THERMAL2.0210
1D2818LOOSE THERMAL1.7810
2E2519LOOSE POSITIONAL0.285
2F2519LOOSE POSITIONAL0.245
2G2519LOOSE POSITIONAL0.265
2H2519LOOSE POSITIONAL0.255
2E2519LOOSE THERMAL1.4910
2F2519LOOSE THERMAL1.310
2G2519LOOSE THERMAL1.3810
2H2519LOOSE THERMAL1.6410
LS refinement shellResolution: 1.979→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 731 -
Rwork0.201 14140 -
all-14871 -
obs--88.52 %
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)
10.4288-0.04120.04250.41810.05630.25640.0007-0.0313-0.0065-0.01160.00420.03110.0218-0.027-0.0048-0.0936-0.01460.0025-0.09060.0205-0.124422.4761.34755.288
20.44410.0071-0.02550.5565-0.0860.25660.01430.05-0.0409-0.0371-0.01310.0517-0.01240.0191-0.0013-0.0846-0.0034-0.0092-0.0732-0.041-0.08326.679-25.548-6.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 361
2X-RAY DIFFRACTION1B1 - 329
3X-RAY DIFFRACTION1C1 - 361
4X-RAY DIFFRACTION1D1 - 329
5X-RAY DIFFRACTION2E1 - 361
6X-RAY DIFFRACTION2F1 - 329
7X-RAY DIFFRACTION2G1 - 361
8X-RAY DIFFRACTION2H1 - 329

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