8I0K: PDB entry 8I0K

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase(E1) with TCAIM complex. Determined by electron microscopy at 2.86 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.86 Å
Organism: Homo sapiens
Chains: 3
Atoms: 16,537
Mol. weight: 243.96 kDa
Ligands: MG, 8EL, CA, TPP
Released: 1 May 2024

Explore 8I0K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I0K contains 94 α-helices and 68 β-strands across 3 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: 43 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	126-140	15
α-helix	141-144	4
α-helix	169-175	7
α-helix	179-183	5
β-strand	185-187	3	1
β-strand	200-202	3	1
α-helix	203-215	13
β-strand	218-221	4	2
α-helix	228-239	12
α-helix	248-271	24
α-helix	286-299	14
β-strand	304-308	5	2
α-helix	314-320	7
α-helix	326-332	7
α-helix	348-350	3
β-strand	353-358	6	2
β-strand	365-370	6	2
α-helix	381-394	14
β-strand	403-410	8	2
α-helix	411-414	4
α-helix	419-426	8
β-strand	438-443	6	2
α-helix	452-454	3
α-helix	464-467	4
β-strand	472-476	5	2
α-helix	480-497	18
β-strand	501-506	6	2
α-helix	519-521	3
α-helix	524-530	7
α-helix	536-547	12
α-helix	552-574	23
α-helix	611-622	12
α-helix	633-647	15
β-strand	650-651	2	3
α-helix	653-666	14
β-strand	670-675	6	4
β-strand	690-691	2	5
β-strand	699-700	2	5
α-helix	702-705	4
β-strand	713-717	5	4
α-helix	718-719	2
α-helix	723-733	11
β-strand	739-744	6	4
α-helix	748-754	7
α-helix	755-757	3
α-helix	758-762	5
α-helix	765-768	4
β-strand	776-780	5	4
α-helix	788-790	3
α-helix	795-799	5
α-helix	818-823	6
β-strand	828-830	3	4
α-helix	835-847	13
β-strand	854-858	5	4
α-helix	861-863	3
β-strand	870-871	2	3
α-helix	872-874	3
β-strand	884-885	2	6
α-helix	895-897	3
β-strand	900-904	5	6
α-helix	908-918	11
β-strand	922	1	6
β-strand	925-930	6	6
α-helix	938-947	10
β-strand	952-960	9	6
α-helix	969-976	8
β-strand	984-988	5	6
α-helix	989-990	2
α-helix	999-1013	15

Chain B: 42 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	126-140	15
α-helix	141-144	4
α-helix	169-175	7
α-helix	179-181	3
β-strand	185-187	3	7
β-strand	200-202	3	7
α-helix	203-214	12
β-strand	218-221	4	8
α-helix	228-239	12
α-helix	248-271	24
α-helix	286-299	14
β-strand	304-308	5	8
α-helix	314-320	7
α-helix	326-332	7
β-strand	353-358	6	8
β-strand	365-370	6	8
α-helix	381-394	14
β-strand	403-410	8	8
α-helix	411-414	4
α-helix	419-426	8
β-strand	438-443	6	8
α-helix	452-454	3
α-helix	464-467	4
β-strand	472-476	5	8
α-helix	480-497	18
β-strand	501-506	6	8
α-helix	519-521	3
α-helix	524-530	7
α-helix	536-547	12
α-helix	552-574	23
α-helix	611-621	11
α-helix	633-647	15
β-strand	650-651	2	9
α-helix	653-666	14
β-strand	670-675	6	10
β-strand	690-691	2	11
β-strand	699-700	2	11
α-helix	702-705	4
β-strand	713-717	5	10
α-helix	718-719	2
α-helix	723-733	11
β-strand	739-744	6	10
α-helix	748-754	7
α-helix	755-757	3
α-helix	758-762	5
α-helix	765-768	4
β-strand	776-780	5	10
α-helix	788-790	3
α-helix	795-800	6
α-helix	817-823	7
β-strand	828-830	3	10
α-helix	835-847	13
β-strand	854-858	5	10
α-helix	861-863	3
β-strand	870-871	2	9
α-helix	872-874	3
β-strand	884-885	2	12
α-helix	890-893	4
β-strand	900-904	5	12
α-helix	908-918	11
β-strand	922	1	13
β-strand	925	1	13
β-strand	926-930	5	12
β-strand	932	1	10
α-helix	938-947	10
β-strand	952-960	9	12
α-helix	969-976	8
β-strand	983-988	6	12
α-helix	989-990	2
α-helix	999-1013	15

Chain C: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	189-226	38
β-strand	231-233	3	14
α-helix	239-255	17
α-helix	260-263	4
β-strand	268-271	4	14
β-strand	276	1	14
β-strand	277	1	15
β-strand	282-285	4	14
α-helix	290-297	8
α-helix	300-320	21
β-strand	325-326	2	16
β-strand	337	1	15
α-helix	338-353	16
β-strand	368-369	2	16
β-strand	379-380	2	16
β-strand	386-387	2	16
α-helix	394-403	10
α-helix	405-433	29
β-strand	437-440	4	17
α-helix	446-456	11
β-strand	468-472	5	17
β-strand	476-477	2	17
β-strand	483-486	4	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-oxoglutarate dehydrogenase complex component E1	A, B	protein	911	Homo sapiens	Q02218 (AlphaFold model)
T-cell activation inhibitor, mitochondrial	C	protein	302	Homo sapiens	Q8N3R3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8I0K_1 2-oxoglutarate dehydrogenase complex component E1 (chains A, B)
LVEAQPNVDKLVEDHLAVQSLIRAYQIRGHHVAQLDPLGILDADLDSSVPADIISSTDKL
GFYGLDESDLDKVFHLPTTTFIGGQESALPLREIIRRLEMAYCQHIGVEFMFINDLEQCQ
WIRQKFETPGIMQFTNEEKRTLLARLVRSTRFEEFLQRKWSSEKRFGLEGCEVLIPALKT
IIDKSSENGVDYVIMGMPHRGRLNVLANVIRKELEQIFCQFDSKLEAADEGSGDVKYHLG
MYHRRINRVTDRNITLSLVANPSHLEAADPVVMGKTKAEQFYCGDTEGKKVMSILLHGDA
AFAGQGIVYETFHLSDLPSYTTHGTVHVVVNNQIGFTTDPRMARSSPYPTDVARVVNAPI
FHVNSDDPEAVMYVCKVAAEWRSTFHKDVVVDLVCYRRNGHNEMDEPMFTQPLMYKQIRK
QKPVLQKYAELLVSQGVVNQPEYEEEISKYDKICEEAFARSKDEKILHIKHWLDSPWPGF
FTLDGQPRSMSCPSTGLTEDILTHIGNVASSVPVENFTIHGGLSRILKTRGEMVKNRTVD
WALAEYMAFGSLLKEGIHIRLSGQDVERGTFSHRHHVLHDQNVDKRTCIPMNHLWPNQAP
YTVCNSSLSEYGVLGFELGFAMASPNALVLWEAQFGDFHNTAQCIIDQFICPGQAKWVRQ
NGIVLLLPHGMEGMGPEHSSARPERFLQMCNDDPDVLPDLKEANFDINQLYDCNWVVVNC
STPGNFFHVLRRQILLPFRKPLIIFTPKSLLRHPEARSSFDEMLPGTHFQRVIPEDGPAA
QNPENVKRLLFCTGKVYYDLTRERKARDMVGQVAITRIEQLSPFPFDLLLKEVQKYPNAE
LAWCQEEHKNQGYYDYVKPRLRTTISRAKPVWYAGRDPAAAPATGNKKTHLTELQRLLDT
AFDLDVFKNFS

Sequence of entity 2 (C), FASTA

>8I0K_2 T-cell activation inhibitor, mitochondrial (chains C)
TTLTSWLDNNGKSAVKKLKNSLPLRKELDRLKDELSHQLQLSDIRWQRSWGIAHRCSQLH
SLSRLAQQNLETLKKAKGCTIIFTDRSGMSAVGHVMLGTMDVHHHWTKLFERLPSYFDLQ
RRLMILEDQISYLLGGIQVVYIEELQPVLTLEEYYSLLDVFYNRLLKSRILFHPRSLRGL
QMILNSDRYAPSLHELGHFNIPTLCDPANLQWFILTKAQQARENMKRKEELKVIENELIQ
ASTKKFSLEKLYKEPSISSIQMVDCCKRLLEQSLPYLHGMHLCISHFYSVMQDGDLCIPW
NW

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
8EL	2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]et…	C12 H20 N4 O7 P2 S	1
CA	Calcium ion	Ca	1
TPP	Thiamine diphosphate	C12 H19 N4 O7 P2 S	1

Primary citation

The mitochondrial DNAJC co-chaperone TCAIM reduces alpha-ketoglutarate dehydrogenase protein levels to regulate metabolism. Wang, J., Yu, X., Zhong, Y. et al. Mol Cell (2025) 85:638. DOI 10.1016/j.molcel.2025.01.006

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…
7WGR 2.92 Å, Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component…

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