PDB-6cer: Human pyruvate dehydrogenase complex E1 component V138M mutation

ID or keywords:

Entry

Database: PDB / ID: 6cer

Title

Human pyruvate dehydrogenase complex E1 component V138M mutation

Components

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Keywords

OXIDOREDUCTASE / pyruvate dehydrogenase deficiency /

mutation /

thiamin diphosphate /

metabolism

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.69 Å

Authors

Whitley, M.J. / Arjunan, P. / Furey, W.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Feb 12, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 11, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 18, 2018	Group: 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 1.2	Sep 5, 2018	Group: 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 1.3	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0	Aug 4, 2021	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6cer.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb6cer.ent.gz	854.9 KB	Display	PDB format
PDBx/mmJSON format	6cer.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ce/6cer ftp://data.pdbj.org/pub/pdb/validation_reports/ce/6cer	HTTPS FTP

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Related structure data

Related structure data	6cfoC 1ni4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3exg-1 3exg-3 3exg-2 3exg-5 3exg-6 3exf-2 3exe-1 2ozl-d 3exg-7 7ecy-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (11) #154 - Oct 2012 Citric Acid Cycle similarity (6) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (2) #155 - Nov 2012 Vitamin D Receptor similarity (2)

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

309 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
Evidence: This complex is long known in the literature to be a heterotetramer.
155 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
Evidence: This complex is long known in the literature to be a heterotetramer.
155 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.760, 123.919, 128.279
Angle α, β, γ (deg.)	90.00, 118.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / PDHE1-A type I Mass: 40746.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: V138 Mutant / Source: (gene. exp.) Homo sapiens (human) / Gene: PDHA1, PHE1A / Production host: Escherichia coli (E. coli) References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial / PDHE1-B Mass: 36085.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDHB, PHE1B / Production host: Escherichia coli (E. coli) References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring)
#3: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S
#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 / Water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.71 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: ammonium sulfate, PEG 3350, potassium phosphate, magnesium chloride, thiamin diphosphate PH range: 6.0-7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2008
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.69→35.69 Å / Num. obs: 89293 / % possible obs: 95.59 % / Redundancy: 2.8 % / CC_1/2: 0.993 / R_merge(I) obs: 0.114 / R_pim(I) all: 0.076 / R_rim(I) all: 0.138 / Net I/σ(I): 8.43
Reflection shell	Resolution: 2.69→2.786 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.684 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 9028 / CC_1/2: 0.726 / R_pim(I) all: 0.456 / R_rim(I) all: 0.825 / % possible all: 96.79

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1NI4

1ni4

Resolution: 2.69→35.686 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2338	4460	5 %
R_work	0.1918	-	-
obs	0.1939	89237	95.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.69→35.686 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20540	0	106	302	20948

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	21062
X-RAY DIFFRACTION	f_angle_d	0.617	28463
X-RAY DIFFRACTION	f_dihedral_angle_d	12.926	12686
X-RAY DIFFRACTION	f_chiral_restr	0.044	3079
X-RAY DIFFRACTION	f_plane_restr	0.004	3723

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6901-2.7206	0.4199	145	0.3478	2768	X-RAY DIFFRACTION	94
2.7206-2.7526	0.3699	153	0.3114	2909	X-RAY DIFFRACTION	98
2.7526-2.7862	0.3308	153	0.3015	2899	X-RAY DIFFRACTION	98
2.7862-2.8214	0.3306	150	0.3079	2856	X-RAY DIFFRACTION	98
2.8214-2.8585	0.3432	152	0.3031	2891	X-RAY DIFFRACTION	98
2.8585-2.8977	0.3381	151	0.2875	2879	X-RAY DIFFRACTION	98
2.8977-2.9391	0.2825	153	0.2745	2895	X-RAY DIFFRACTION	98
2.9391-2.9829	0.3026	151	0.2593	2866	X-RAY DIFFRACTION	98
2.9829-3.0295	0.327	151	0.2644	2870	X-RAY DIFFRACTION	97
3.0295-3.0791	0.3349	150	0.2693	2851	X-RAY DIFFRACTION	98
3.0791-3.1322	0.2949	152	0.2508	2891	X-RAY DIFFRACTION	97
3.1322-3.1891	0.2929	148	0.2469	2829	X-RAY DIFFRACTION	97
3.1891-3.2504	0.3445	153	0.2427	2889	X-RAY DIFFRACTION	97
3.2504-3.3167	0.2757	149	0.2303	2840	X-RAY DIFFRACTION	97
3.3167-3.3888	0.24	150	0.2165	2840	X-RAY DIFFRACTION	97
3.3888-3.4676	0.2964	149	0.2057	2841	X-RAY DIFFRACTION	97
3.4676-3.5542	0.2288	149	0.2043	2836	X-RAY DIFFRACTION	96
3.5542-3.6502	0.2434	150	0.1938	2842	X-RAY DIFFRACTION	96
3.6502-3.7575	0.2171	148	0.1853	2801	X-RAY DIFFRACTION	96
3.7575-3.8786	0.2407	148	0.1686	2823	X-RAY DIFFRACTION	95
3.8786-4.0171	0.2241	148	0.1696	2806	X-RAY DIFFRACTION	95
4.0171-4.1777	0.1868	147	0.1524	2789	X-RAY DIFFRACTION	95
4.1777-4.3675	0.1847	148	0.143	2827	X-RAY DIFFRACTION	95
4.3675-4.5973	0.1565	147	0.128	2794	X-RAY DIFFRACTION	94
4.5973-4.8847	0.1559	146	0.1236	2761	X-RAY DIFFRACTION	94
4.8847-5.2607	0.179	146	0.1357	2786	X-RAY DIFFRACTION	93
5.2607-5.7881	0.1792	145	0.1505	2743	X-RAY DIFFRACTION	93
5.7881-6.6211	0.2102	144	0.1609	2730	X-RAY DIFFRACTION	92
6.6211-8.3243	0.1942	143	0.1518	2725	X-RAY DIFFRACTION	91
8.3243-35.6888	0.1715	141	0.1602	2700	X-RAY DIFFRACTION	88

Refinement TLS params.

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

ID	L11 (°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)
1	1.1253	0.232	-0.0945	0.4618	0.0501	1.8356	-0.0691	0.373	-0.1369	-0.091	-0.0068	-0.0021	-0.0559	0.055	0.0663	0.338	0.0664	-0.0249	0.7375	-0.0727	0.3363	-19.8335	-0.3779	19.9409
2	0.9688	0.2058	-0.0202	0.8171	0.0294	0.9438	-0.0885	-0.0209	-0.1634	0.0707	0.0385	-0.1999	0.1243	0.5261	0.0517	0.3304	0.1406	-0.0178	0.8635	0.0179	0.3769	-0.0702	-1.1982	47.878
3	0.1029	0.1965	-0.1112	2.067	-0.8803	2.4057	0.0186	-0.1955	-0.1089	0.2881	0.0126	-0.1037	0.1293	0.1756	-0.0373	0.3763	0.085	-0.0349	0.8411	0.0462	0.3284	-10.0501	0.8673	71.3968
4	1.4869	0.3614	0.1935	0.8879	-0.1058	0.8363	-0.0494	0.062	0.3136	-0.0557	-0.0277	-0.1341	-0.7863	0.6102	0.0922	0.7524	-0.2626	-0.0604	0.8797	0.0488	0.4295	4.1191	33.7288	44.2545
5	1.3275	0.2662	-0.2464	1.2904	0.1663	1.9868	0.0034	0.1457	0.195	-0.089	-0.0009	0.1382	-0.4792	-0.1129	-0.0184	0.4735	0.1828	-0.0369	0.6552	0.0273	0.279	-27.5111	22.7244	45.8281
6	0.4803	-0.0296	-0.3865	0.9671	0.3684	2.9808	-0.043	-0.1834	-0.1281	0.1361	-0.0194	0.1363	-0.0754	-0.1847	0.0463	0.3213	0.1134	0.0015	0.8345	0.0278	0.3378	-34.5651	4.4758	62.4316
7	0.8853	0.2602	-0.2948	0.7618	-0.2691	0.8901	-0.0129	-0.5439	-0.2002	0.1061	0.033	0.072	0.3016	-0.0259	-0.0337	0.4771	0	-0.0499	0.7234	0.0724	0.3671	27.8565	-35.1848	24.9085
8	1.7236	0.3027	0.3729	1.1413	-0.5938	2.0081	-0.0189	0.095	-0.2621	-0.1479	0.0477	-0.0811	0.4193	0.3442	-0.0167	0.3363	0.1059	-0.0398	0.4139	-0.0759	0.2837	46.7095	-24.7768	-1.5154
9	2.4907	-0.8	0.1015	0.8317	0.2077	0.1043	0.0311	0.0693	0.0524	0.0452	-0.0115	-0.1784	-0.0286	0.6323	0.0013	0.3211	-0.0067	-0.0171	0.905	-0.0444	0.3548	64.6269	-6.5805	1.2266
10	0.9532	-0.201	0.4795	0.521	-0.2452	1.503	0.1172	0.1781	0.018	-0.0195	-0.0102	0.0654	-0.0488	-0.3083	-0.0966	0.3025	0.0712	-0.0035	0.6318	-0.0153	0.2875	20.8682	-1.0732	-8.6852
11	1.5203	-0.2227	0.2633	0.9036	-0.3955	1.7061	-0.0638	-0.4027	0.1249	0.2076	0.0449	0.0345	-0.1292	-0.2933	0.0376	0.3295	0.0662	-0.0197	0.624	-0.1041	0.2919	33.8226	-0.3765	22.3574
12	0.9723	0.2595	0.9977	1.5128	0.0958	1.0486	-0.0803	-0.2998	0.1439	0.1738	-0.0144	-0.0842	-0.1461	0.4712	0.1131	0.4032	0.0041	-0.0766	0.9647	-0.1061	0.3538	59.0098	-2.5514	26.5969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 361 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 0 through 194 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 195 through 329 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 2 through 361 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid -1 through 194 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 195 through 329 )
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 0 through 361 )
8	X-RAY DIFFRACTION	8	chain 'F' and (resid 0 through 194 )
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 195 through 329 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid -2 through 361 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid -1 through 194 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 195 through 329 )

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