9J9B: Substrate-engaged TIM23 complex from yeast

Substrate-engaged TIM23 complex from yeast. Determined by electron microscopy at 3.83 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.83 Å
Organisms: Saccharomyces cerevisiae S288C, synthetic construct
Chains: 7
Atoms: 6,047
Mol. weight: 191.12 kDa
Ligands: CDL
Released: 10 Sept 2025

Explore 9J9B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J9B contains 27 α-helices and 31 β-strands across 7 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	14-40	27
α-helix	46-83	38
α-helix	89-102	14
α-helix	108-135	28

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	98-121	24
α-helix	131-165	35

Chain C: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	102-104	3
α-helix	105-124	20
α-helix	127-146	20
α-helix	148-151	4
α-helix	154-163	10
α-helix	166-171	6
α-helix	177-192	16
α-helix	258-262	5
α-helix	263-265	3
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	337-356	20	1
β-strand	363-379	17	1
β-strand	385-387	3	1
β-strand	394-404	11	1
β-strand	417-424	8	1

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	15-45	31
α-helix	52-76	25

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	139-147	9

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	2
β-strand	31	1	3
α-helix	32	1
β-strand	37-44	8	2
β-strand	52-59	8	4
β-strand	63-70	8	4
β-strand	76-78	3	4
β-strand	86-91	6	2
β-strand	96-101	6	2
α-helix	106-108	3
β-strand	110-117	8	4
β-strand	123-126	4	4
β-strand	130-132	3	4
β-strand	134	1	3

Chain L: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	5
β-strand	30-33	4	6
β-strand	39-44	6	5
β-strand	50-51	2	7
β-strand	54-55	2	7
β-strand	57-62	6	6
β-strand	69-73	5	6
β-strand	77-78	2	6
β-strand	86-91	6	5
β-strand	94-99	6	5
α-helix	102-103	2
β-strand	109-114	6	6
β-strand	122	1	6
β-strand	126-130	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial import inner membrane translocase subunit TIM17	A	protein	158	Saccharomyces cerevisiae S288C	P39515 (AlphaFold model)
Mitochondrial import inner membrane translocase subunit TIM23	B	protein	222	Saccharomyces cerevisiae S288C	P32897 (AlphaFold model)
Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase…	C	protein	757	Saccharomyces cerevisiae S288C, synthetic construct	P00175 (AlphaFold model), Q01852 (AlphaFold model)
Protein MGR2	D	protein	113	Saccharomyces cerevisiae S288C	Q02889
anti-Tim44-Fab H chain	H	protein	238	Saccharomyces cerevisiae S288C
anti-Tim44-Fab L chain	L	protein	238	Saccharomyces cerevisiae S288C
Substrate	E	protein	15	Saccharomyces cerevisiae S288C

Sequence of entity 1 (A), FASTA

>9J9B_1 Mitochondrial import inner membrane translocase subunit TIM17 (chains A)
MSADHSRDPCPIVILNDFGGAFAMGAIGGVVWHGIKGFRNSPLGERGSGAMSAIKARAPV
LGGNFGVWGGLFSTFDCAVKAVRKREDPWNAIIAGFFTGGALAVRGGWRHTRNSSITCAC
LLGVIEGVGLMFQRYAAWQAKPMAPPLPEAPSSQPLQA

Sequence of entity 2 (B), FASTA

>9J9B_2 Mitochondrial import inner membrane translocase subunit TIM23 (chains B)
MSWLFGDKTPTDDANAAVGGQDTTKPKELSLKQSLGFEPNINNIISGPGGMHVDTARLHP
LAGLDKGVEYLDLEEEQLSSLEGSQGLIPSRGWTDDLCYGTGAVYLLGLGIGGFSGMMQG
LQNIPPNSPGKLQLNTVLNHITKRGPFLGNNAGILALSYNIINSTIDALRGKHDTAGSIG
AGALTGALFKSSKGLKPMGYSSAMVAAACAVWCSVKKRLLEK

Sequence of entity 3 (C), FASTA

>9J9B_3 Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP (chains C)
MHRSTFIRTSGTSSRTLTARYRSQYTGLLVARVLFSTSTTRAQGGNPRSPLQIFRDTFKK
EWEKSQELQENIKTLQDASGKLGESEAYKKAREAYLKAQRGSTIVGKTLKKTGETMEHIA
TKAWESELGKNTRKAAAATAKKLDESFEPVRQTKIYKEVSEVIDDGESSRYGGFITKEQR
RLKRERDLASGKRHRAVKSNEDAGTAVVATNIESKESFGKKVEDFKEKTVVGRSIQSLKN
KLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPE
ILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQ
DIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKIL
EFVRGGSRQFTPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSGS
GSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTL
VTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLV
NRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLAD
HYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGSAGLEVLF
QGPANGGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 4 (D), FASTA

>9J9B_4 Protein MGR2 (chains D)
MPPLPQNYAQQQPSNWDKFKMGLMMGTTVGVCTGILFGGFAIATQGPGPDGVVRTLGKYI
AGSAGTFGLFMSIGSIIRSDSESSPMSHPNLNLQQQARLEMWKLRAKYGIRKD

Sequence of entity 5 (H), FASTA

>9J9B_5 anti-Tim44-Fab H chain (chains H)
MDWTWRVFCLLAVAPGAHSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSP
GKGLEWLGVMWRGGSTDFNAAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCARYGNY
DAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSG
SLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 6 (L), FASTA

>9J9B_6 anti-Tim44-Fab L chain (chains L)
MVLQTQVFISLLLWISGAYGDIVLTQSPASLAVSLGQRATISCRASESVDIYGISFMNWF
QQKPGQPPKLLIYATSNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPR
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 7 (E), FASTA

>9J9B_7 Substrate (chains E)
XXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
CDL	Cardiolipin	C81 H156 O17 P2	1

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 P39515 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8E1M 2.9 Å, Cryo-EM structure of the endogenous core TIM23 complex from S. cerevisiae
9N84 3.2 Å, Yeast TIM23 complex inhibited by stendomycin

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