9EII: PDB entry 9EII

Import stalled PINK1 TOM complex, symmetry expanded. Determined by electron microscopy at 2.75 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 13
Atoms: 14,448
Mol. weight: 268.13 kDa
Ligands: PC1
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

9EII contains 64 α-helices and 73 β-strands across 13 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 B: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	64-66	3
β-strand	69	1	1
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	2
β-strand	168-174	7	2
β-strand	216-221	6	2
α-helix	230-236	7
β-strand	244	1	2
α-helix	248-250	3
β-strand	274	1	3
β-strand	277-282	6	2
β-strand	314-319	6	2
β-strand	323-324	2	3
α-helix	325-331	7
α-helix	336-356	21
β-strand	359	1	4
β-strand	368-372	5	3
β-strand	378-382	5	3
α-helix	385-387	3
β-strand	389	1	4
β-strand	397-399	3	5
α-helix	416-419	4
β-strand	428-430	3	5
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 D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	17-28	12
α-helix	33-52	20
α-helix	63-83	21
α-helix	86-99	14
α-helix	103-111	9
α-helix	116-125	10
α-helix	126-128	3

Chain F: 5 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	6
β-strand	50-59	10	6
β-strand	64-75	12	6
β-strand	80-87	8	6
β-strand	91-98	8	6
β-strand	106-115	10	6
α-helix	116-118	3
β-strand	120-131	12	6
β-strand	134-141	8	6
β-strand	148-155	8	6
β-strand	160-169	10	6
β-strand	174-185	12	6
β-strand	189-196	8	6
β-strand	200-207	8	6
β-strand	213-222	10	6
β-strand	227-239	13	6
β-strand	242-249	8	6
β-strand	253-263	11	6
β-strand	266-275	10	6
α-helix	279-281	3
β-strand	285-293	9	6

Chain I: 3 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	100-110	11	1
β-strand	113-121	9	1
β-strand	128-140	13	1
β-strand	146-155	10	1
β-strand	161-167	7	1
β-strand	173-181	9	1
β-strand	184-195	12	1
β-strand	199-201	3	1
β-strand	204-206	3	1
β-strand	215-226	12	1
β-strand	229-240	12	1
β-strand	243-256	14	1
β-strand	259-266	8	1
β-strand	269-276	8	1
β-strand	282-291	10	1
β-strand	296-307	12	1
β-strand	312-319	8	1
β-strand	323-331	9	1
β-strand	338-346	9	1
β-strand	351-360	10	1

Chain J: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	83-86	4
α-helix	88-91	4
α-helix	95-97	3
β-strand	100-110	11	7
β-strand	113-121	9	7
β-strand	128-140	13	7
β-strand	146-155	10	7
β-strand	160-169	10	7
β-strand	172-181	10	7
β-strand	184-195	12	7
β-strand	199-209	11	7
β-strand	214-226	13	7
β-strand	229-240	12	7
β-strand	243-256	14	7
β-strand	259-266	8	7
β-strand	269-276	8	7
β-strand	282-291	10	7
β-strand	297-307	11	7
α-helix	308-310	3
β-strand	312-319	8	7
β-strand	323-331	9	7
β-strand	337-346	10	7
β-strand	351-360	10	7

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	15-45	31

Chain N: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-38	33
α-helix	45-47	3
α-helix	49-53	5

Chains P and V: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	41-61	21

4 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
Serine/threonine-protein kinase PINK1, mitochondrial	B	protein	603	Homo sapiens	Q9BXM7 (AlphaFold model)
Mitochondrial import receptor subunit TOM20 homolog	D	protein	145	Homo sapiens	Q15388 (AlphaFold model)
Voltage-dependent anion-selective channel protein 2	F	protein	294	Homo sapiens	P45880 (AlphaFold model)
Mitochondrial import receptor subunit TOM40 homolog	I, J	protein	361	Homo sapiens	O96008 (AlphaFold model)
Mitochondrial import receptor subunit TOM5 homolog	L, Z	protein	51	Homo sapiens	Q8N4H5
Mitochondrial import receptor subunit TOM7 homolog	N, X	protein	55	Homo sapiens	Q9P0U1
Mitochondrial import receptor subunit TOM6 homolog	P, V	protein	74	Homo sapiens	Q96B49
Mitochondrial import receptor subunit TOM22 homolog	R, T	protein	142	Homo sapiens	Q9NS69

Sequence of entity 1 (B), FASTA

>9EII_1 Serine/threonine-protein kinase PINK1, mitochondrial (chains B)
MAVRQALGRGLQLGRALLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRVG
LGLPNRLRFFRQSVAGLAARLQRQFVVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRR
AVSACQEIQAIFTQKSKPGPDPLDTRRLQGFRLEEYLIGQSIGKGCSAAVYEATMPTLPQ
NLEVTKSTGLLPGRGPGTSAPGEGQERAPGAPAFPLAIKMMWNISAGSSSEAILNTMSQE
LVPASRVALAGEYGAVTYRKSKRGPKQLAPHPNIIRVLRAFTSSVPLLPGALVDYPDVLP
SRLHPEGLGHGRTLFLVMKNYPCTLRQYLCVNTPSPRLAAMMLLQLLEGVDHLVQQGIAH
RDLKSDNILVELDPDGCPWLVIADFGCCLADESIGLQLPFSSWYVDRGGNGCLMAPEVST
ARPGPRAVIDYSKADAWAVGAIAYEIFGLVNPFYGQGKAHLESRSYQEAQLPALPESVPP
DVRQLVRALLQREASKRPSARVAANVLHLSLWGEHILALKNLKLDKMVGWLLQQSAATLL
ANRLTEKCCVETKMKMLFLANLECETLCQAALLLCSWRAALDYKDHDGDYKDHDIDYKDD
DDK

Sequence of entity 2 (D), FASTA

>9EII_2 Mitochondrial import receptor subunit TOM20 homolog (chains D)
MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDL
KDAEAVQKFFLEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQ
MLLTKLPTISQRIVSAQSLAEDDVE

Sequence of entity 3 (F), FASTA

>9EII_3 Voltage-dependent anion-selective channel protein 2 (chains F)
MATHGQTCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNT
DTGKVTGTLETKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGK
KSGKIKSSYKRECINLGCDVDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNF
AVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNLAWTSGTNCTRFGIAAKYQLDP
TASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGHKVGLALELEA

Sequence of entity 4 (I, J), FASTA

>9EII_4 Mitochondrial import receptor subunit TOM40 homolog (chains I, J)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
G

Sequence of entity 5 (L, Z), FASTA

>9EII_5 Mitochondrial import receptor subunit TOM5 homolog (chains L, Z)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI

Sequence of entity 6 (N, X), FASTA

>9EII_6 Mitochondrial import receptor subunit TOM7 homolog (chains N, X)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG

Sequence of entity 7 (P, V), FASTA

>9EII_7 Mitochondrial import receptor subunit TOM6 homolog (chains P, V)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV

Sequence of entity 8 (R, T), FASTA

>9EII_8 Mitochondrial import receptor subunit TOM22 homolog (chains R, T)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI

Ligands and cofactors

ID	Name	Formula	Copies
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	9

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 Q9BXM7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9KQN 2.84 Å, Hsp90-Cdc37-PINK1 complex
9KMR 2.98 Å, Human Hsp90-PINK1 complex
9EIH 3.1 Å, Import stalled PINK1 TOM complex
9EIJ 3.3 Å, Import stalled PINK1 TOM complex, extended TOM20 helix class
9KOX 4.43 Å, human Hsp90-FKBP51-PINK1 complex

Browse structure collections

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