8XKX: TOM40 complex with pre-protein

Structure of the TOM40 complex with pre-protein. Determined by electron microscopy at 3.7 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Saccharomyces cerevisiae
Chains: 10
Atoms: 7,518
Mol. weight: 161.09 kDa
Released: 25 Dec 2024

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

Secondary structure: helices and β-sheets

8XKX contains 22 α-helices and 46 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.

Chains A and F: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	50-53	4
α-helix	59-62	4
α-helix	68-71	4
β-strand	84-93	10	1
β-strand	97-106	10	1
β-strand	114-121	8	1
β-strand	125-132	8	1
β-strand	136-143	8	1
β-strand	149-158	10	1
β-strand	164-172	9	1
β-strand	176-187	12	1
β-strand	193-206	14	1
β-strand	209-219	11	1
α-helix	225-227	3
β-strand	228-237	10	1
β-strand	243-249	7	1
β-strand	255	1	1
β-strand	257-262	6	1
β-strand	267-273	7	1
β-strand	301-308	8	1
β-strand	312-319	8	1
β-strand	324-330	7	1
β-strand	337	1	2
β-strand	338-345	8	1
β-strand	350-355	6	1
β-strand	358	1	2
β-strand	359-362	4	1
α-helix	365-372	8

Chains B and G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	87-134	48

Chains C and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-48	35

Chains D and I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	31-50	20
α-helix	52-57	6

Chains E and J: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-43	32
α-helix	50-54	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial import receptor subunit TOM22	B, G	protein	172	Saccharomyces cerevisiae	P49334 (AlphaFold model)
Mitochondrial import receptor subunit TOM5	C, H	protein	50	Saccharomyces cerevisiae	P80967 (AlphaFold model)
Mitochondrial import receptor subunit TOM6	D, I	protein	61	Saccharomyces cerevisiae	P33448 (AlphaFold model)
Mitochondrial import receptor subunit TOM7	E, J	protein	60	Saccharomyces cerevisiae	P53507 (AlphaFold model)
Mitochondrial import receptor subunit TOM40	A, F	protein	387	Saccharomyces cerevisiae	P23644

Sequence of entity 1 (B, G), FASTA

>8XKX_1 Mitochondrial import receptor subunit TOM22 (chains B, G)
MVELTEIKDDVVQLDEPQFSRNQAIVEEKASATNNDVVDDEDDSDSDFEDEFDENETLLD
RIVALKDIVPPGKRQTISNFFGFTSSFVRNAFTKSGNLAWTLTTTALLLGVPLSLSILAE
QQLIEMEKTFDLQSDANNILAQGEKDAAATANRTLQVDGSPGHHHHHHHHHH

Sequence of entity 2 (C, H), FASTA

>8XKX_2 Mitochondrial import receptor subunit TOM5 (chains C, H)
MFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK

Sequence of entity 3 (D, I), FASTA

>8XKX_3 Mitochondrial import receptor subunit TOM6 (chains D, I)
MDGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAPQ
L

Sequence of entity 4 (E, J), FASTA

>8XKX_4 Mitochondrial import receptor subunit TOM7 (chains E, J)
MSFLPSFILSDESKERISKILTLTHNVAHYGWIPFVLYLGWAHTSNRPNFLNLLSPLPSV

Sequence of entity 5 (A, F), FASTA

>8XKX_5 Mitochondrial import receptor subunit TOM40 (chains A, F)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL

Primary citation

Structure of the TOM40 complex with pre-protein. Yang, L.Y., Shen, Q.T. To be published.

Other PDB entries of the same protein (UniProt P49334 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9J99 2.94 Å, Substrate-engaged TOM complex from yeast
6UCU 3.06 Å, Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer)
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
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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