9EIH: Import stalled PINK1 TOM complex

Import stalled PINK1 TOM complex. Determined by electron microscopy at 3.1 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 26
Atoms: 28,887
Mol. weight: 535.47 kDa
Ligands: PC1
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

9EIH contains 128 α-helices and 151 β-strands across 26 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: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	64-66	3
α-helix	71-73	3
α-helix	77-90	14
β-strand	91	1	5
α-helix	108-135	28
α-helix	138-141	4
α-helix	142-144	3
α-helix	153-155	3
β-strand	157-165	9	9
β-strand	168-174	7	9
β-strand	216-221	6	9
α-helix	230-237	8
β-strand	244	1	10
α-helix	246-250	5
β-strand	274	1	11
β-strand	277	1	10
β-strand	279-283	5	9
β-strand	313-319	7	9
β-strand	323-324	2	11
α-helix	325-331	7
α-helix	336-356	21
β-strand	359	1	12
β-strand	368-372	5	11
β-strand	378-382	5	11
α-helix	385-387	3
β-strand	389	1	12
β-strand	397-399	3	13
β-strand	405	1	14
α-helix	416-419	4
β-strand	428-430	3	13
α-helix	434-446	13
α-helix	450-451	2
α-helix	457-459	3
α-helix	472-475	4
α-helix	480-489	10
α-helix	498-499	2
α-helix	500-512	13
α-helix	514-517	4
α-helix	524-543	20
α-helix	548-549	2
α-helix	550-560	11
α-helix	566-578	13

Chain B: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	64-66	3
β-strand	69	1	7
α-helix	71-73	3
α-helix	77-90	14
α-helix	108-135	28
α-helix	138-141	4
α-helix	142-144	3
α-helix	153-155	3
β-strand	157-164	8	15
β-strand	168-174	7	15
β-strand	216-221	6	15
α-helix	230-236	7
β-strand	244	1	16
α-helix	248-250	3
β-strand	274	1	17
β-strand	277	1	16
β-strand	279-282	4	15
β-strand	314-319	6	15
β-strand	323-324	2	17
α-helix	325-331	7
α-helix	336-356	21
β-strand	359	1	18
β-strand	368-372	5	17
β-strand	378-382	5	17
α-helix	385-387	3
β-strand	389	1	18
β-strand	397-399	3	19
β-strand	405	1	14
α-helix	416-419	4
β-strand	428-430	3	19
α-helix	434-446	13
α-helix	449-451	3
α-helix	457-459	3
α-helix	468-470	3
α-helix	472-475	4
α-helix	480-489	10
α-helix	494-496	3
α-helix	498-499	2
α-helix	500-512	13
α-helix	514-517	4
α-helix	524-544	21
α-helix	550-560	11
α-helix	564-578	15

Chain C: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	17-19	3
α-helix	21-30	10
α-helix	32-51	20
α-helix	55-59	5
α-helix	63-82	20
α-helix	86-97	12
α-helix	103-110	8
α-helix	116-125	10
α-helix	126-130	5

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	17-28	12
α-helix	33-52	20
α-helix	63-82	20
α-helix	86-99	14
α-helix	103-111	9
α-helix	116-125	10
α-helix	126-128	3

Chain E: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	18-20	3
α-helix	23-30	8
β-strand	37-45	9	1
β-strand	51-59	9	1
β-strand	64-72	9	1
β-strand	80-87	8	1
β-strand	91-103	13	1
β-strand	106-115	10	1
β-strand	120-131	12	1
β-strand	134-142	9	1
β-strand	148-155	8	1
α-helix	157-159	3
β-strand	160-169	10	1
β-strand	174-185	12	1
β-strand	189-196	8	1
β-strand	200-208	9	1
β-strand	213-221	9	1
β-strand	229-239	11	1
β-strand	242-249	8	1
β-strand	253-263	11	1
β-strand	266-275	10	1
α-helix	279-281	3
β-strand	285-293	9	1

Chain F: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
α-helix	18-20	3
α-helix	23-30	8
β-strand	37-45	9	2
β-strand	50-59	10	2
β-strand	64-75	12	2
β-strand	80-87	8	2
β-strand	91-98	8	2
β-strand	106-115	10	2
α-helix	116-118	3
β-strand	120-131	12	2
β-strand	134-141	8	2
β-strand	148-155	8	2
β-strand	160-169	10	2
β-strand	174-185	12	2
β-strand	189-196	8	2
β-strand	200-210	11	2
β-strand	213-222	10	2
β-strand	227-239	13	2
β-strand	242-249	8	2
β-strand	253-263	11	2
β-strand	266-275	10	2
β-strand	285-292	8	2

Chain G: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	83-85	3
α-helix	88-91	4
β-strand	100-110	11	3
β-strand	113-121	9	3
β-strand	128-135	8	3
β-strand	140-142	3	4
β-strand	145-147	3	4
β-strand	149-155	7	3
β-strand	160-169	10	3
β-strand	172-181	10	3
β-strand	184-195	12	3
β-strand	199-209	11	3
β-strand	214-224	11	3
β-strand	229-240	12	3
β-strand	243-256	14	3
β-strand	259-266	8	3
β-strand	269-276	8	3
β-strand	282-291	10	3
β-strand	297-307	11	3
α-helix	308-310	3
β-strand	312-319	8	3
β-strand	323-332	10	3
β-strand	337-346	10	3
β-strand	351-360	10	3

Chain H: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	83-85	3
α-helix	88-91	4
α-helix	95-97	3
β-strand	98	1	5
β-strand	100-110	11	6
β-strand	113-121	9	6
β-strand	128-142	15	6
β-strand	145-155	11	6
β-strand	160-169	10	6
β-strand	172-181	10	6
β-strand	184-195	12	6
β-strand	199-209	11	6
β-strand	214-226	13	6
β-strand	229-240	12	6
β-strand	243-254	12	6
β-strand	259-266	8	6
β-strand	269-276	8	6
β-strand	282-291	10	6
β-strand	296-307	12	6
α-helix	308-310	3
β-strand	312-319	8	6
β-strand	323-332	10	6
β-strand	337-346	10	6
β-strand	351-360	10	6

15 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial import receptor subunit TOM20 homolog	C, D	protein	145	Homo sapiens	Q15388 (AlphaFold model)
Non-selective voltage-gated ion channel VDAC2	E, F	protein	294	Homo sapiens	P45880 (AlphaFold model)
Mitochondrial import receptor subunit TOM40 homolog	G, H, I, J	protein	361	Homo sapiens	O96008 (AlphaFold model)
Mitochondrial import receptor subunit TOM5 homolog	K, L, Y, Z	protein	51	Homo sapiens	Q8N4H5 (AlphaFold model)
Mitochondrial import receptor subunit TOM7 homolog	M, N, W, X	protein	55	Homo sapiens	Q9P0U1
Mitochondrial import receptor subunit TOM6 homolog	O, P, U, V	protein	74	Homo sapiens	Q96B49
Mitochondrial import receptor subunit TOM22 homolog	Q, R, S, T	protein	142	Homo sapiens	Q9NS69
Serine/threonine-protein kinase PINK1, mitochondrial	A, B	protein	603	Homo sapiens	Q9BXM7

Sequence of entity 1 (C, D), FASTA

>9EIH_1 Mitochondrial import receptor subunit TOM20 homolog (chains C, D)
MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDL
KDAEAVQKFFLEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQ
MLLTKLPTISQRIVSAQSLAEDDVE

Sequence of entity 2 (E, F), FASTA

>9EIH_2 Non-selective voltage-gated ion channel VDAC2 (chains E, F)
MATHGQTCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNT
DTGKVTGTLETKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGK
KSGKIKSSYKRECINLGCDVDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNF
AVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNLAWTSGTNCTRFGIAAKYQLDP
TASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGHKVGLALELEA

Sequence of entity 3 (G, H, I, J), FASTA

>9EIH_3 Mitochondrial import receptor subunit TOM40 homolog (chains G, H, I, J)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
G

Sequence of entity 4 (K, L, Y, Z), FASTA

>9EIH_4 Mitochondrial import receptor subunit TOM5 homolog (chains K, L, Y, Z)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI

Sequence of entity 5 (M, N, W, X), FASTA

>9EIH_5 Mitochondrial import receptor subunit TOM7 homolog (chains M, N, W, X)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG

Sequence of entity 6 (O, P, U, V), FASTA

>9EIH_6 Mitochondrial import receptor subunit TOM6 homolog (chains O, P, U, V)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV

Sequence of entity 7 (Q, R, S, T), FASTA

>9EIH_7 Mitochondrial import receptor subunit TOM22 homolog (chains Q, R, S, T)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI

Sequence of entity 8 (A, B), FASTA

>9EIH_8 Serine/threonine-protein kinase PINK1, mitochondrial (chains A, B)
MAVRQALGRGLQLGRALLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRVG
LGLPNRLRFFRQSVAGLAARLQRQFVVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRR
AVSACQEIQAIFTQKSKPGPDPLDTRRLQGFRLEEYLIGQSIGKGCSAAVYEATMPTLPQ
NLEVTKSTGLLPGRGPGTSAPGEGQERAPGAPAFPLAIKMMWNISAGSSSEAILNTMSQE
LVPASRVALAGEYGAVTYRKSKRGPKQLAPHPNIIRVLRAFTSSVPLLPGALVDYPDVLP
SRLHPEGLGHGRTLFLVMKNYPCTLRQYLCVNTPSPRLAAMMLLQLLEGVDHLVQQGIAH
RDLKSDNILVELDPDGCPWLVIADFGCCLADESIGLQLPFSSWYVDRGGNGCLMAPEVST
ARPGPRAVIDYSKADAWAVGAIAYEIFGLVNPFYGQGKAHLESRSYQEAQLPALPESVPP
DVRQLVRALLQREASKRPSARVAANVLHLSLWGEHILALKNLKLDKMVGWLLQQSAATLL
ANRLTEKCCVETKMKMLFLANLECETLCQAALLLCSWRAALDYKDHDGDYKDHDIDYKDD
DDK

Ligands and cofactors

ID	Name	Formula	Copies
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	17

Primary citation

Structure of human PINK1 at a mitochondrial TOM-VDAC array. Callegari, S., Kirk, N.S., Gan, Z.Y. et al. Science (2025) 388:303-310. DOI 10.1126/science.adu6445 · PubMed

Other PDB entries of the same protein (UniProt Q15388 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4APO 1.9 Å, AIP TPR domain in complex with human Tomm20 peptide
7VBY 2.54 Å, Tom core complex with Tom20 and Tom22 subunits.
9EII 2.75 Å, Import stalled PINK1 TOM complex, symmetry expanded
8UY3 3.2 Å, Fem1B with FNIP1 and Tom20 fragment
9EIJ 3.3 Å, Import stalled PINK1 TOM complex, extended TOM20 helix class
9JCE 3.59 Å, local refinement of FEM1B bound with TOM20
9J79 4.08 Å, Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer)
9J7B 4.12 Å, local refinement of FEM1B bound with TOM20(tetramer)
9J7A 4.13 Å, local refinement of FEM1B bound with TOM20 (dimer)
8XVA 5.92 Å, Human TOM complex with whole Tom20
7VC9 13.0 Å, Tom20 subunits

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