9J99: Substrate-engaged TOM complex from yeast

Substrate-engaged TOM complex from yeast. Determined by electron microscopy at 2.94 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 2.94 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 10
Atoms: 8,859
Mol. weight: 180.13 kDa
Ligands: UND, PC1
Released: 10 Sept 2025

Explore 9J99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J99 contains 29 α-helices and 38 β-strands across 10 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: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	52-55	4
α-helix	68	1
α-helix	69-74	6
β-strand	83-91	9	1
β-strand	98-106	9	1
β-strand	114-122	9	1
β-strand	125-132	8	1
β-strand	137-146	10	1
β-strand	149-157	9	1
α-helix	162-163	2
β-strand	164-172	9	1
β-strand	176-187	12	1
β-strand	193-204	12	1
β-strand	209-219	11	1
β-strand	227-237	11	1
β-strand	243-249	7	1
β-strand	255-262	8	1
β-strand	267-278	12	1
β-strand	296-308	13	1
β-strand	312-319	8	1
β-strand	323-333	11	1
β-strand	336-345	10	1
β-strand	350-362	13	1
α-helix	365-372	8

Chains B and J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	88-134	47

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-48	38

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	25-28	4
α-helix	31-49	19
α-helix	55-57	3

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	25-31	7
α-helix	32-41	10
α-helix	50-53	4

Chain I: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	52-55	4
α-helix	57-59	3
α-helix	68	1
α-helix	69-74	6
β-strand	83-91	9	2
β-strand	98-106	9	2
β-strand	114-122	9	2
β-strand	125-132	8	2
β-strand	137-144	8	2
β-strand	149-157	9	2
α-helix	162-163	2
β-strand	164-172	9	2
β-strand	176-187	12	2
β-strand	193-204	12	2
β-strand	209-219	11	2
β-strand	229-237	9	2
β-strand	243-249	7	2
β-strand	254-262	9	2
β-strand	267-279	13	2
β-strand	295-308	14	2
β-strand	312-319	8	2
β-strand	323-333	11	2
β-strand	336-345	10	2
β-strand	350-362	13	2
α-helix	365-372	8
α-helix	376-378	3

Chain K: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-48	37

Chain L: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	25-28	4
α-helix	31-50	20
α-helix	53-56	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial import receptor subunit TOM40	A, I	protein	387	Saccharomyces cerevisiae S288C	P23644 (AlphaFold model)
Mitochondrial import receptor subunit TOM22	B, J	protein	152	Saccharomyces cerevisiae S288C	P49334 (AlphaFold model)
Mitochondrial import receptor subunit TOM5	C, K	protein	50	Saccharomyces cerevisiae S288C	P80967 (AlphaFold model)
Mitochondrial import receptor subunit TOM6	D, L	protein	61	Saccharomyces cerevisiae S288C	P33448 (AlphaFold model)
Mitochondrial import receptor subunit TOM7	E, M	protein	60	Saccharomyces cerevisiae S288C	P53507

Sequence of entity 1 (A, I), FASTA

>9J99_1 Mitochondrial import receptor subunit TOM40 (chains A, I)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL

Sequence of entity 2 (B, J), FASTA

>9J99_2 Mitochondrial import receptor subunit TOM22 (chains B, J)
MVELTEIKDDVVQLDEPQFSRNQAIVEEKASATNNDVVDDEDDSDSDFEDEFDENETLLD
RIVALKDIVPPGKRQTISNFFGFTSSFVRNAFTKSGNLAWTLTTTALLLGVPLSLSILAE
QQLIEMEKTFDLQSDANNILAQGEKDAAATAN

Sequence of entity 3 (C, K), FASTA

>9J99_3 Mitochondrial import receptor subunit TOM5 (chains C, K)
MFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK

Sequence of entity 4 (D, L), FASTA

>9J99_4 Mitochondrial import receptor subunit TOM6 (chains D, L)
MDGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAPQ
L

Sequence of entity 5 (E, M), FASTA

>9J99_5 Mitochondrial import receptor subunit TOM7 (chains E, M)
MSFLPSFILSDESKERISKILTLTHNVAHYGWIPFVLYLGWAHTSNRPNFLNLLSPLPSV

Ligands and cofactors

ID	Name	Formula	Copies
UND	Undecane	C11 H24	26
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	25

Primary citation

Dynamic TOM-TIM23 supercomplex directs mitochondrial protein translocation and sorting. Yang, Y., Wang, S., Wang, G. et al. Nat Struct Mol Biol (2025) 32:2231-2241. DOI 10.1038/s41594-025-01662-x · PubMed

Other PDB entries of the same protein (UniProt P23644 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7E4H 3.01 Å, Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom
7E4I 3.05 Å, Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom
6UCU 3.06 Å, Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer)
7VKU 3.2 Å, Cryo-EM structure of SAM-Tom40 intermediate complex
8XKY 3.42 Å, Structure of the TOM40 complex annealed
8W5K 3.6 Å, Cryo-EM structure of the yeast TOM core complex crosslinked by BS3 (from TOM-TIM23…
8XKW 3.64 Å, Structure of the TOM40 complex unannealed
8XKX 3.7 Å, Structure of the TOM40 complex with pre-protein
6JNF 3.81 Å, Cryo-EM structure of the translocator of the outer mitochondrial membrane
6UCV 4.1 Å, Cryo-EM structure of the mitochondrial TOM complex from yeast (tetramer)
8HCO 4.1 Å, Substrate-engaged TOM complex from yeast
8W5J 4.4 Å, Cryo-EM structure of the yeast TOM core complex (from TOM-TIM23 complex)

Browse structure collections

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