9N84: Yeast TIM23 complex inhibited by stendomycin

Yeast TIM23 complex inhibited by stendomycin. Determined by electron microscopy at 3.2 Å resolution. Released 16 Sept 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Saccharomyces cerevisiae, Mus musculus, synthetic construct
Chains: 6
Atoms: 5,854
Mol. weight: 144.31 kDa
Ligands: M12, PTY, CDL
Released: 16 Sept 2026

Explore 9N84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N84 contains 31 α-helices and 35 β-strands across 6 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	10-27	18
α-helix	31-40	10
α-helix	43-45	3
α-helix	46-83	38
α-helix	89-101	13
α-helix	104-106	3
α-helix	108-137	30

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	93-122	30
α-helix	124-125	2
α-helix	130-170	41
α-helix	175-189	15
α-helix	196-219	24

Chain C: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	108-125	18
α-helix	127-152	26
α-helix	154-163	10
α-helix	167-171	5
α-helix	177-186	10
α-helix	187-191	5
α-helix	256-265	10
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	2
β-strand	342-357	16	1
β-strand	362-374	13	1
β-strand	377-379	3	2
β-strand	385-387	3	2
β-strand	393-404	12	1
β-strand	417-425	9	1
β-strand	429	1	1

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9

Chain H: 3 helices, 12 β-strands

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

Chain L: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	3
β-strand	30-32	3	4
β-strand	39-45	7	3
β-strand	50-51	2	5
β-strand	54-55	2	5
β-strand	57-62	6	4
β-strand	69-73	5	4
β-strand	77-78	2	4
β-strand	86-91	6	3
β-strand	94-99	6	3
β-strand	109-114	6	4
α-helix	120	1
β-strand	121	1	6
β-strand	122	1	4
β-strand	126-129	4	4

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
Stendomycin V	D	protein	14	synthetic construct

Sequence of entity 1 (A), FASTA

>9N84_1 Mitochondrial import inner membrane translocase subunit TIM17 (chains A)
MSADHSRDPCPIVILNDFGGAFAMGAIGGVVWHGIKGFRNSPLGERGSGAMSAIKARAPV
LGGNFGVWGGLFSTFDCAVKAVRKREDPWNAIIAGFFTGGALAVRGGWRHTRNSSITCAC
LLGVIEGVGLMFQRYAAWQAKPMAPPLPEAPSSQPLQA

Sequence of entity 2 (B), FASTA

>9N84_2 Mitochondrial import inner membrane translocase subunit TIM23 (chains B)
MSWLFGDKTPTDDANAAVGGQDTTKPKELSLKQSLGFEPNINNIISGPGGMHVDTARLHP
LAGLDKGVEYLDLEEEQLSSLEGSQGLIPSRGWTDDLCYGTGAVYLLGLGIGGFSGMMQG
LQNIPPNSPGKLQLNTVLNHITKRGPFLGNNAGILALSYNIINSTIDALRGKHDTAGSIG
AGALTGALFKSSKGLKPMGYSSAMVAAACAVWCSVKKRLLEK

Sequence of entity 3 (C), FASTA

>9N84_3 Mitochondrial import inner membrane translocase subunit TIM44 (chains C)
MHRSTFIRTSGTSSRTLTARYRSQYTGLLVARVLFSTSTTRAQGGNPRSPLQIFRDTFKK
EWEKSQELQENIKTLQDASGKLGESEAYKKAREAYLKAQRGSTIVGKTLKKTGETMEHIA
TKAWESELGKNTRKAAAATAKKLDESFEPVRQTKIYKEVSEVIDDGESSRYGGFITKEQR
RLKRERDLASGKRHRAVKSNEDAGTAVVATNIESKESFGKKVEDFKEKTVVGRSIQSLKN
KLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPE
ILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQ
DIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKIL
EFVRGGSRQFT

Sequence of entity 4 (L), FASTA

>9N84_4 Antibody Fab fragment light chain (chains L)
MEKDTLLLWVLLLWVPGSTGDIVLTQSPASLAVSLGQRATISCRASESVDIYGISFMNWF
QQKPGQPPKLLIYATSNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPR
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (H), FASTA

>9N84_5 Antibody Fab fragment heavy chain (chains H)
MAVLVLLLCLVTFPSCVLSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSP
GKGLEWLGVMWRGGSTDFNAAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCARYGNY
DAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSG
SLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 6 (D), FASTA

>9N84_6 Stendomycin V (chains D)
PTGVXATTVVTSXX

Ligands and cofactors

ID	Name	Formula	Copies
M12	10-methylundecanoic acid	C12 H24 O2	1
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	1
CDL	Cardiolipin	C81 H156 O17 P2	1

Primary citation

Topogenic sequence recognition at TIM complexes revealed by a stendomycin-bound structure. Chen, Y., Lurie, A., Wu, K. et al. Nat Chem Biol (2026). DOI 10.1038/s41589-026-02304-z · 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
9J9B 3.83 Å, Substrate-engaged TIM23 complex from yeast

Browse structure collections

About this viewer

MolViewer shows 9N84 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.