8W5K: Yeast TOM core complex crosslinked by BS3

Cryo-EM structure of the yeast TOM core complex crosslinked by BS3 (from TOM-TIM23 complex). Determined by electron microscopy at 3.6 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 10
Atoms: 7,379
Mol. weight: 156.94 kDa
Ligands: 46E
Released: 13 Mar 2024

Explore 8W5K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W5K contains 25 α-helices and 39 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 B and J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	87-134	48

Chains C and K: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-48	35

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

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

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	20-43	24
α-helix	50-54	5

Chain F: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	50-54	5
α-helix	59-62	4
α-helix	63-65	3
α-helix	68-71	4
β-strand	83-93	11	1
β-strand	97-106	10	1
β-strand	114-121	8	1
β-strand	125-132	8	1
β-strand	136-144	9	1
β-strand	149-157	9	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	225-226	2
β-strand	227-237	11	1
β-strand	243-249	7	1
β-strand	255-264	10	1
β-strand	267-275	9	1
β-strand	299-308	10	1
β-strand	312-319	8	1
β-strand	323-330	8	1
β-strand	336-345	10	1
β-strand	350-359	10	1
β-strand	361-362	2	1
α-helix	365-372	8

Chain I: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	50-54	5
α-helix	59-62	4
α-helix	63-65	3
α-helix	68-72	5
β-strand	83-93	11	2
β-strand	97-106	10	2
β-strand	114-121	8	2
β-strand	125-132	8	2
β-strand	138-144	7	2
β-strand	150-156	7	2
β-strand	164-172	9	2
β-strand	176-187	12	2
β-strand	193-206	14	2
β-strand	209-218	10	2
α-helix	225-226	2
β-strand	227-237	11	2
β-strand	243-249	7	2
β-strand	255-261	7	2
β-strand	267-275	9	2
β-strand	299-308	10	2
β-strand	312-319	8	2
β-strand	323-330	8	2
β-strand	336-345	10	2
β-strand	350-362	13	2
α-helix	365-372	8

Chain M: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	20-30	11
α-helix	32-43	12
α-helix	50-54	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial import receptor subunit TOM22	B, J	protein	152	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P49334 (AlphaFold model)
Mitochondrial import receptor subunit TOM5	C, K	protein	50	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P80967 (AlphaFold model)
Mitochondrial import receptor subunit TOM6	D, L	protein	61	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33448 (AlphaFold model)
Mitochondrial import receptor subunit TOM7	E, M	protein	60	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53507 (AlphaFold model)
Mitochondrial import receptor subunit TOM40	F, I	protein	387	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23644

Sequence of entity 1 (B, J), FASTA

>8W5K_1 Mitochondrial import receptor subunit TOM22 (chains B, J)
MVELTEIKDDVVQLDEPQFSRNQAIVEEKASATNNDVVDDEDDSDSDFEDEFDENETLLD
RIVALKDIVPPGKRQTISNFFGFTSSFVRNAFTKSGNLAWTLTTTALLLGVPLSLSILAE
QQLIEMEKTFDLQSDANNILAQGEKDAAATAN

Sequence of entity 2 (C, K), FASTA

>8W5K_2 Mitochondrial import receptor subunit TOM5 (chains C, K)
MFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK

Sequence of entity 3 (D, L), FASTA

>8W5K_3 Mitochondrial import receptor subunit TOM6 (chains D, L)
MDGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAPQ
L

Sequence of entity 4 (E, M), FASTA

>8W5K_4 Mitochondrial import receptor subunit TOM7 (chains E, M)
MSFLPSFILSDESKERISKILTLTHNVAHYGWIPFVLYLGWAHTSNRPNFLNLLSPLPSV

Sequence of entity 5 (F, I), FASTA

>8W5K_5 Mitochondrial import receptor subunit TOM40 (chains F, I)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL

Ligands and cofactors

ID	Name	Formula	Copies
46E	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl…	C33 H66 N O8 P	1

Primary citation

The architecture of substrate-engaged TOM-TIM23 supercomplex reveals preprotein proximity sites for mitochondrial protein translocation. Wang, Q., Zhuang, J., Huang, R. et al. Cell Discov (2024) 10:19-19. DOI 10.1038/s41421-023-00643-y · PubMed

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
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

About this viewer

MolViewer shows 8W5K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.