7VDD: Human TOM complex with cross-linking

Human TOM complex with cross-linking. Determined by electron microscopy at 3.74 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 3.74 Å
Organism: Homo sapiens
Chains: 10
Atoms: 8,204
Mol. weight: 147.54 kDa
Released: 13 Jul 2022

Explore 7VDD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VDD contains 33 α-helices and 39 β-strands across 10 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: 2 helices, 0 β-strands

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

Chain B: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	88-91	4
α-helix	95-97	3
β-strand	100-108	9	1
β-strand	113-121	9	1
β-strand	128-142	15	1
β-strand	145-155	11	1
β-strand	160-169	10	1
β-strand	172-180	9	1
β-strand	185-195	11	1
β-strand	199-209	11	1
β-strand	214-224	11	1
β-strand	229-238	10	1
β-strand	245-255	11	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
α-helix	308-310	3
β-strand	312-319	8	1
β-strand	323-331	9	1
β-strand	338-346	9	1
β-strand	351-359	9	1

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-13	11
α-helix	30-40	11
α-helix	45-54	10
α-helix	59-62	4
α-helix	64-95	32
α-helix	97-117	21

Chains D and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	16-47	32

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	41-60	20

Chain G: 3 helices, 0 β-strands

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

Chain H: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-10	8
α-helix	30-40	11
α-helix	45-54	10
α-helix	59-62	4
α-helix	64-95	32
α-helix	97-117	21

Chain I: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	84-87	4
α-helix	88-91	4
α-helix	95-97	3
β-strand	100-110	11	2
β-strand	113-121	9	2
β-strand	128-140	13	2
β-strand	146-155	10	2
β-strand	160-165	6	2
β-strand	169	1	2
β-strand	172-180	9	2
β-strand	185-195	11	2
β-strand	199-209	11	2
β-strand	214-224	11	2
β-strand	229-240	12	2
β-strand	243-256	14	2
β-strand	259-266	8	2
β-strand	269-276	8	2
β-strand	282-291	10	2
β-strand	296-307	12	2
α-helix	308-310	3
β-strand	312-319	8	2
β-strand	323-331	9	2
β-strand	338-346	9	2
β-strand	351-360	10	2

1 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 TOM6 homolog	A, F	protein	74	Homo sapiens	Q96B49 (AlphaFold model)
Mitochondrial import receptor subunit TOM22 homolog	C, H	protein	142	Homo sapiens	Q9NS69 (AlphaFold model)
Mitochondrial import receptor subunit TOM5 homolog	D, E	protein	51	Homo sapiens	Q8N4H5 (AlphaFold model)
Mitochondrial import receptor subunit TOM7 homolog	G, J	protein	55	Homo sapiens	Q9P0U1 (AlphaFold model)
Mitochondrial import receptor subunit TOM40 homolog	B, I	protein	361	Homo sapiens	O96008

Sequence of entity 1 (A, F), FASTA

>7VDD_1 Mitochondrial import receptor subunit TOM6 homolog (chains A, F)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV

Sequence of entity 2 (C, H), FASTA

>7VDD_2 Mitochondrial import receptor subunit TOM22 homolog (chains C, H)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI

Sequence of entity 3 (D, E), FASTA

>7VDD_3 Mitochondrial import receptor subunit TOM5 homolog (chains D, E)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI

Sequence of entity 4 (G, J), FASTA

>7VDD_4 Mitochondrial import receptor subunit TOM7 homolog (chains G, J)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG

Sequence of entity 5 (B, I), FASTA

>7VDD_5 Mitochondrial import receptor subunit TOM40 homolog (chains B, I)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
G

Primary citation

Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors. Su, J., Liu, D., Yang, F. et al. Proc Natl Acad Sci U S A (2022) 119:e2200158119-e2200158119. DOI 10.1073/pnas.2200158119 · PubMed

Other PDB entries of the same protein (UniProt Q96B49 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VD2 2.53 Å, Human TOM complex without cross-linking
7VBY 2.54 Å, Tom core complex with Tom20 and Tom22 subunits.
9EII 2.75 Å, Import stalled PINK1 TOM complex, symmetry expanded
9JXV 2.89 Å, human translocase of the outer mitochondrial membrane (TOM complex)
8XDN 2.93 Å, TOM complex with small molecule
9WV3 2.98 Å, Human TOM complex with substrate Tim22-GGC1-sfGFP
7CP9 3.0 Å, Cryo-EM structure of human mitochondrial translocase TOM complex at 3.0 angstrom.
9EIH 3.1 Å, Import stalled PINK1 TOM complex
9WV2 3.15 Å, Human TOM complex with substrate GGC1-sfGFP
9EIJ 3.3 Å, Import stalled PINK1 TOM complex, extended TOM20 helix class
7CK6 3.4 Å, Protein translocase of mitochondria
7VC4 3.74 Å, Tom complex with Tom22 and Tom20 subunits

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