7WGR: 2-oxoglutarate dehydrogenase, mitochondrial

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex. Determined by electron microscopy at 2.92 Å resolution. Released 1 Jun 2022.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Homo sapiens
Chains: 2
Atoms: 13,614
Mol. weight: 204.99 kDa
Ligands: TPP, MG, CA
Released: 1 Jun 2022

Explore 7WGR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WGR contains 81 α-helices and 55 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 41 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	130-144	15
α-helix	169-174	6
α-helix	179-181	3
β-strand	185-187	3	1
β-strand	200-202	3	1
α-helix	203-214	12
β-strand	218-221	4	2
α-helix	228-239	12
α-helix	248-271	24
α-helix	277-279	3
α-helix	286-300	15
β-strand	304-308	5	2
α-helix	314-316	3
α-helix	317-321	5
α-helix	326-334	9
β-strand	343-345	3	2
β-strand	367-370	4	2
α-helix	381-395	15
β-strand	403-410	8	2
α-helix	419-428	10
α-helix	430-432	3
β-strand	438-443	6	2
β-strand	447	1	3
β-strand	450	1	3
α-helix	452-454	3
α-helix	463-465	3
β-strand	472-476	5	2
α-helix	480-497	18
β-strand	501-506	6	2
α-helix	524-530	7
α-helix	536-547	12
α-helix	552-573	22
α-helix	604-606	3
α-helix	611-621	11
α-helix	633-647	15
β-strand	650-651	2	4
α-helix	653-666	14
β-strand	670-675	6	5
β-strand	690-691	2	6
β-strand	699-700	2	6
α-helix	702-705	4
β-strand	713-717	5	5
α-helix	724-735	12
β-strand	739-744	6	5
α-helix	750-754	5
α-helix	755-757	3
α-helix	758-762	5
β-strand	776-780	5	5
α-helix	795-799	5
α-helix	819-824	6
β-strand	828-830	3	5
α-helix	835-847	13
β-strand	854-858	5	5
β-strand	870-871	2	4
α-helix	872-874	3
α-helix	890-893	4
α-helix	895-897	3
β-strand	899-904	6	7
α-helix	908-919	12
β-strand	922	1	7
β-strand	925-929	5	7
β-strand	932-934	3	5
α-helix	940-947	8
β-strand	954-960	7	7
α-helix	966-976	11
β-strand	984-988	5	7
α-helix	989-990	2
α-helix	999-1014	16
α-helix	1020-1022	3

Chain B: 40 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	130-140	11
α-helix	141-143	3
α-helix	169-174	6
α-helix	179-181	3
β-strand	185-187	3	8
β-strand	200-202	3	8
α-helix	203-214	12
β-strand	218-221	4	9
α-helix	228-238	11
α-helix	248-271	24
α-helix	286-300	15
β-strand	304-308	5	9
α-helix	314-316	3
α-helix	317-321	5
α-helix	326-334	9
β-strand	343-345	3	9
β-strand	367-370	4	9
α-helix	381-395	15
β-strand	403-410	8	9
α-helix	413-415	3
α-helix	419-425	7
β-strand	438-443	6	9
β-strand	447	1	10
β-strand	450	1	10
α-helix	463-468	6
β-strand	472-476	5	9
α-helix	480-497	18
β-strand	501-506	6	9
α-helix	524-530	7
α-helix	536-547	12
α-helix	552-573	22
α-helix	604-606	3
α-helix	611-621	11
α-helix	633-647	15
β-strand	650-651	2	11
α-helix	653-666	14
β-strand	670-675	6	12
β-strand	690-691	2	13
β-strand	699-700	2	13
α-helix	702-705	4
β-strand	713-715	3	12
α-helix	724-735	12
β-strand	739-744	6	12
α-helix	750-754	5
α-helix	755-757	3
α-helix	758-762	5
β-strand	776-780	5	12
α-helix	795-800	6
α-helix	818-823	6
β-strand	828-830	3	12
α-helix	835-847	13
β-strand	854-858	5	12
β-strand	870-871	2	11
α-helix	872-874	3
α-helix	890-893	4
α-helix	895-897	3
β-strand	899-904	6	14
α-helix	908-918	11
β-strand	925-929	5	14
β-strand	932-934	3	12
α-helix	938-945	8
β-strand	954-956	3	14
α-helix	966-976	11
β-strand	984-986	3	14
α-helix	988-990	3
α-helix	999-1012	14
α-helix	1020-1022	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-oxoglutarate dehydrogenase, mitochondrial	A, B	protein	895	Homo sapiens	Q02218 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7WGR_1 2-oxoglutarate dehydrogenase, mitochondrial (chains A, B)
AVQSLIRAYQIRGHHVAQLDPLGILDADLDSSVPADIISSTDKLGFYGLDESDLDKVFHL
PTTTFIGGQESALPLREIIRRLEMAYCQHIGVEFMFINDLEQCQWIRQKFETPGIMQFTN
EEKRTLLARLVRSTRFEEFLQRKWSSEKRFGLEGCEVLIPALKTIIDKSSENGVDYVIMG
MPHRGRLNVLANVIRKELEQIFCQFDSKLEAADEGSGDVKYHLGMYHRRINRVTDRNITL
SLVANPSHLEAADPVVMGKTKAEQFYCGDTEGKKVMSILLHGDAAFAGQGIVYETFHLSD
LPSYTTHGTVHVVVNNQIGFTTDPRMARSSPYPTDVARVVNAPIFHVNSDDPEAVMYVCK
VAAEWRSTFHKDVVVDLVCYRRNGHNEMDEPMFTQPLMYKQIRKQKPVLQKYAELLVSQG
VVNQPEYEEEISKYDKICEEAFARSKDEKILHIKHWLDSPWPGFFTLDGQPRSMSCPSTG
LTEDILTHIGNVASSVPVENFTIHGGLSRILKTRGEMVKNRTVDWALAEYMAFGSLLKEG
IHIRLSGQDVERGTFSHRHHVLHDQNVDKRTCIPMNHLWPNQAPYTVCNSSLSEYGVLGF
ELGFAMASPNALVLWEAQFGDFHNTAQCIIDQFICPGQAKWVRQNGIVLLLPHGMEGMGP
EHSSARPERFLQMCNDDPDVLPDLKEANFDINQLYDCNWVVVNCSTPGNFFHVLRRQILL
PFRKPLIIFTPKSLLRHPEARSSFDEMLPGTHFQRVIPEDGPAAQNPENVKRLLFCTGKV
YYDLTRERKARDMVGQVAITRIEQLSPFPFDLLLKEVQKYPNAELAWCQEEHKNQGYYDY
VKPRLRTTISRAKPVWYAGRDPAAAPATGNKKTHLTELQRLLDTAFDLDVFKNFS

Ligands and cofactors

ID	Name	Formula	Copies
TPP	Thiamine diphosphate	C12 H19 N4 O7 P2 S	2
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	2

Primary citation

Structural basis for the activity and regulation of human alpha-ketoglutarate dehydrogenase revealed by Cryo-EM. Zhong, Y., Gao, Y., Zhou, D. et al. Biochem Biophys Res Commun (2022) 602:120-126. DOI 10.1016/j.bbrc.2022.02.093

Other PDB entries of the same protein (UniProt Q02218 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
8I0K 2.86 Å, Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase(E1) with TCAIM…

Browse structure collections

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