8E1M: Endogenous core TIM23 complex from S. cerevisiae

Cryo-EM structure of the endogenous core TIM23 complex from S. cerevisiae. Determined by electron microscopy at 2.9 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Saccharomyces cerevisiae, Mus musculus
Chains: 5
Atoms: 5,691
Mol. weight: 142.67 kDa
Ligands: CDL, PTY
Released: 21 Jun 2023

Explore 8E1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E1M contains 30 α-helices and 32 β-strands across 5 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	10-40	31
α-helix	43-45	3
α-helix	48-83	36
α-helix	89-101	13
α-helix	108-137	30

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	93-121	29
α-helix	124-125	2
α-helix	130-168	39
α-helix	175-189	15
α-helix	196-219	24

Chain C: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	108-125	18
α-helix	127-151	25
α-helix	154-163	10
α-helix	167-171	5
α-helix	177-186	10
α-helix	187-191	5
α-helix	256-264	9
α-helix	269-280	12
α-helix	286-292	7
α-helix	293-297	5
α-helix	298-307	10
α-helix	310-316	7
β-strand	317	1	1
α-helix	319-334	16
β-strand	337-339	3	1
β-strand	342-357	16	1
β-strand	362-379	18	1
β-strand	385-404	20	1
β-strand	417-425	9	1
β-strand	429	1	1

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	5
β-strand	31	1	6
α-helix	32	1
β-strand	37-44	8	5
β-strand	52-59	8	7
β-strand	63-70	8	7
β-strand	76-78	3	7
β-strand	86-91	6	5
β-strand	96-101	6	5
α-helix	106-108	3
β-strand	110-117	8	7
α-helix	119-121	3
β-strand	125-126	2	7
β-strand	130-132	3	7
β-strand	134	1	6

Chain L: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	2
β-strand	30-33	4	3
β-strand	39-44	6	2
β-strand	50-51	2	4
β-strand	54-55	2	4
β-strand	57-62	6	3
β-strand	69-73	5	3
β-strand	77-78	2	3
α-helix	79	1
β-strand	86-91	6	2
β-strand	94-99	6	2
α-helix	102-103	2
β-strand	109-114	6	3
α-helix	120	1
β-strand	121-122	2	3
β-strand	126-130	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial import inner membrane translocase subunit TIM17	A	protein	158	Saccharomyces cerevisiae	P39515 (AlphaFold model)
Mitochondrial import inner membrane translocase subunit TIM23	B	protein	222	Saccharomyces cerevisiae	P32897 (AlphaFold model)
Mitochondrial import inner membrane translocase subunit TIM44	C	protein	431	Saccharomyces cerevisiae	Q01852 (AlphaFold model)
Antibody Fab fragment light chain	L	protein	238	Mus musculus
Antibody Fab fragment heavy chain	H	protein	238	Mus musculus

Sequence of entity 1 (A), FASTA

>8E1M_1 Mitochondrial import inner membrane translocase subunit TIM17 (chains A)
MSADHSRDPCPIVILNDFGGAFAMGAIGGVVWHGIKGFRNSPLGERGSGAMSAIKARAPV
LGGNFGVWGGLFSTFDCAVKAVRKREDPWNAIIAGFFTGGALAVRGGWRHTRNSSITCAC
LLGVIEGVGLMFQRYAAWQAKPMAPPLPEAPSSQPLQA

Sequence of entity 2 (B), FASTA

>8E1M_2 Mitochondrial import inner membrane translocase subunit TIM23 (chains B)
MSWLFGDKTPTDDANAAVGGQDTTKPKELSLKQSLGFEPNINNIISGPGGMHVDTARLHP
LAGLDKGVEYLDLEEEQLSSLEGSQGLIPSRGWTDDLCYGTGAVYLLGLGIGGFSGMMQG
LQNIPPNSPGKLQLNTVLNHITKRGPFLGNNAGILALSYNIINSTIDALRGKHDTAGSIG
AGALTGALFKSSKGLKPMGYSSAMVAAACAVWCSVKKRLLEK

Sequence of entity 3 (C), FASTA

>8E1M_3 Mitochondrial import inner membrane translocase subunit TIM44 (chains C)
MHRSTFIRTSGTSSRTLTARYRSQYTGLLVARVLFSTSTTRAQGGNPRSPLQIFRDTFKK
EWEKSQELQENIKTLQDASGKLGESEAYKKAREAYLKAQRGSTIVGKTLKKTGETMEHIA
TKAWESELGKNTRKAAAATAKKLDESFEPVRQTKIYKEVSEVIDDGESSRYGGFITKEQR
RLKRERDLASGKRHRAVKSNEDAGTAVVATNIESKESFGKKVEDFKEKTVVGRSIQSLKN
KLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPE
ILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQ
DIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKIL
EFVRGGSRQFT

Sequence of entity 4 (L), FASTA

>8E1M_4 Antibody Fab fragment light chain (chains L)
MEKDTLLLWVLLLWVPGSTGDIVLTQSPASLAVSLGQRATISCRASESVDIYGISFMNWF
QQKPGQPPKLLIYATSNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPR
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (H), FASTA

>8E1M_5 Antibody Fab fragment heavy chain (chains H)
MAVLVLLLCLVTFPSCVLSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSP
GKGLEWLGVMWRGGSTDFNAAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCARYGNY
DAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSG
SLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Ligands and cofactors

ID	Name	Formula	Copies
CDL	Cardiolipin	C81 H156 O17 P2	1
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	1

Primary citation

Structural basis of mitochondrial protein import by the TIM23 complex. Sim, S.I., Chen, Y., Lynch, D.L. et al. Nature (2023) 621:620-626. DOI 10.1038/s41586-023-06239-6 · PubMed

Other PDB entries of the same protein (UniProt P39515 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9N84 3.2 Å, Yeast TIM23 complex inhibited by stendomycin
9J9B 3.83 Å, Substrate-engaged TIM23 complex from yeast

Browse structure collections

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