7E4I: Yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex

Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom. Determined by electron microscopy at 3.05 Å resolution. Released 1 Sept 2021.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 6
Atoms: 11,336
Mol. weight: 189.11 kDa
Released: 1 Sept 2021

Explore 7E4I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E4I contains 62 α-helices and 67 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: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	30-37	8	1
α-helix	44-55	12
α-helix	61-77	17
β-strand	85-87	3	1
β-strand	109-115	7	1
β-strand	124-132	9	2
β-strand	136-146	11	2
α-helix	147-148	2
β-strand	156-164	9	2
β-strand	168-181	14	2
β-strand	184-196	13	2
α-helix	199-201	3
β-strand	203-216	14	2
β-strand	235-251	17	2
α-helix	264-267	4
β-strand	271-287	17	2
β-strand	295-306	12	2
β-strand	310-322	13	2
β-strand	329-342	14	2
α-helix	345-347	3
α-helix	350-352	3
α-helix	353-355	3
β-strand	357	1	3
β-strand	361	1	4
β-strand	365	1	4
β-strand	368	1	5
β-strand	376	1	6
β-strand	381	1	6
β-strand	384	1	3
β-strand	386-396	11	2
α-helix	401-403	3
β-strand	408-420	13	2
α-helix	427-433	7
β-strand	441-449	9	2
β-strand	454-462	9	2
β-strand	464-466	3	7
β-strand	471	1	5
β-strand	474-480	7	2

Chain B: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
β-strand	21-23	3	7
α-helix	24-26	3
α-helix	31-36	6
β-strand	41-43	3	8
α-helix	44	1
β-strand	45-46	2	9
β-strand	60-64	5	8
β-strand	67-69	3	10
β-strand	76-78	3	10
α-helix	81-94	14
β-strand	96-97	2	9
β-strand	102	1	8
α-helix	103-105	3
β-strand	114-117	4	8
α-helix	120-122	3
β-strand	130-133	4	8
β-strand	139-141	3	8
α-helix	143-151	9
α-helix	158-166	9
α-helix	167-171	5
α-helix	172-177	6
α-helix	178-182	5
α-helix	185-191	7
α-helix	204-224	21
α-helix	230-233	4
α-helix	240-242	3
α-helix	249-272	24
α-helix	284-296	13
α-helix	304-311	8
α-helix	314-324	11

Chain C: 22 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	11	1	12
β-strand	14	1	12
α-helix	20-29	10
α-helix	35-41	7
β-strand	46-47	2	11
α-helix	52-54	3
β-strand	62-64	3	11
β-strand	70-72	3	11
α-helix	74-82	9
β-strand	100	1	13
α-helix	105-107	3
α-helix	108-117	10
α-helix	118-122	5
α-helix	123-127	5
α-helix	128-132	5
α-helix	134-136	3
α-helix	137-141	5
α-helix	142-148	7
α-helix	151-153	3
α-helix	156-167	12
α-helix	201-207	7
α-helix	209-240	32
β-strand	248	1	13
α-helix	252-262	11
α-helix	268-279	12
α-helix	281-295	15
β-strand	304	1	11
α-helix	306-308	3
α-helix	309-311	3
α-helix	315-326	12

Chain D: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	51-55	5
α-helix	57-60	4
α-helix	63-65	3
α-helix	68	1
α-helix	69-74	6
β-strand	83-93	11	14
β-strand	97-106	10	14
β-strand	114-121	8	14
β-strand	125-132	8	14
β-strand	136-144	9	14
β-strand	149-157	9	14
β-strand	164-172	9	14
β-strand	176-187	12	14
β-strand	193-206	14	14
β-strand	209-219	11	14
α-helix	225-226	2
β-strand	227-237	11	14
β-strand	243-249	7	14
β-strand	255-264	10	14
β-strand	267-275	9	14
β-strand	299-308	10	14
β-strand	312-319	8	14
β-strand	323-330	8	14
β-strand	337-345	9	14
β-strand	350-362	13	14
α-helix	365-372	8

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-48	35

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	31-50	20
α-helix	52-57	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sorting assembly machinery 50 kDa subunit	A	protein	485	Saccharomyces cerevisiae S288c	P53969 (AlphaFold model)
Sorting assembly machinery 35 kDa subunit	B	protein	329	Saccharomyces cerevisiae S288c	P14693 (AlphaFold model)
Sorting assembly machinery 37 kDa subunit	C	protein	351	Saccharomyces cerevisiae S288c	P50110 (AlphaFold model)
Mitochondrial import receptor subunit TOM40	D	protein	406	Saccharomyces cerevisiae S288c	P23644 (AlphaFold model)
Mitochondrial import receptor subunit TOM5	E	protein	52	Saccharomyces cerevisiae S288c	P80967
Mitochondrial import receptor subunit TOM6	F	protein	62	Saccharomyces cerevisiae S288c	P33448

Sequence of entity 1 (A), FASTA

>7E4I_1 Sorting assembly machinery 50 kDa subunit (chains A)
MATSSSGVDNEISLDSPMPIFNESSTLKPIRVAGVVTTGTDHIDPSVLQAYLDDTIMKSI
TLGQLVKNADVLNKRLCQHHIALNAKQSFHFQGNTYISDEKETHDVVPLMEVVSQLDILP
PKTFTAKTGTNFGNDNDAEAYLQFEKLIDKKYLKLPTRVNLEILRGTKIHSSFLFNSYSS
LSPQSILNLKVFSQFYNWNTNKGLDIGQRGARLSLRYEPLFLHKLLHNPHSNESPTLFHE
WFLETCWRSTKICSQGTSAPYMYSGTMLSQAGDQLRTILGHTFVLDKRDHIMCPTKGSML
KWSNELSPGKHLKTQLELNSVKSWMNDDFITFSTTIKTGYLKNLSSQQSLPVHICDKFQS
GGPSDIRGFQTFGLGPRDLYDAVGGDAFVSYGLSVFSRLPWKKVEKSNFRLHWFFNGGKL
VNHDNTSLGNCIGQLSKEHSTSTGIGLVLRHPMARFELNFTLPITAHENDLIRKGFQFGL
GLAFL

Sequence of entity 2 (B), FASTA

>7E4I_2 Sorting assembly machinery 35 kDa subunit (chains B)
MVSSFSVPMPVKRIFDTFPLQTYAAQTDKDEAVALEIQRRSYTFTERGGGSSELTVEGTY
KLGVYNVFLEANTGAALATDPWCLFVQLALCQKNGLVLPTHSQEQTPSHTCNHEMLVLSR
LSNPDEALPILVEGYKKRIIRSTVAISEIMRSRILDDAEQLMYYTLLDTVLYDCWITQII
FCASDAQFMELYSCQKLSGSIVTPLDVENSLLQKLSAKSLKISLTKRNKFQFRHREIVKS
MQGVYHNHHNSVNQEQVLNVLFENSKQVLLGLKDMLKSDGQPTYLHLKIASYILCITNVK
EPIKLKTFVENECKELVQFAQDTLKNFVQ

Sequence of entity 3 (C), FASTA

>7E4I_3 Sorting assembly machinery 37 kDa subunit (chains C)
MVKGSVHLWGKDGKASLISVDSIALVWFIKLCTSEEAKSMVAGLQIVFSNNTDLSSDGKL
PVLILDNGTKVSGYVNIVQFLHKNICTSKYEKGTDYEEDLAIVRKKDRLLEYSLLNYVDV
EISRLTDYQLFLNTKNYNEYTKKLFSKLLYFPMWYNTPLQLRSQARENCEEIIGSLTLED
DEEFVESKAMESASQLAQSKTFKIAHKNKIKGKQELQQVKYNLQFDNRLQSCVSNWLAAR
KKLDDSVILSSDLLFLANLYVQLGLPDGNRIRSKLEQTFGSELLNSMSNKIDDFVHRPSN
NLEQRDPQFREQGNVVMSLYNLACKYILEDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 4 (D), FASTA

>7E4I_4 Mitochondrial import receptor subunit TOM40 (chains D)
MASAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVN
PGTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSAL
FANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVN
VKTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSK
KQDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEG
STTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQF
ETAGNQELLMLQQGLDADGNPLQALPQLLESAGKPIPNPLLGLDST

Sequence of entity 5 (E), FASTA

>7E4I_5 Mitochondrial import receptor subunit TOM5 (chains E)
MAMFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK

Sequence of entity 6 (F), FASTA

>7E4I_6 Mitochondrial import receptor subunit TOM6 (chains F)
MADGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAP
QL

Primary citation

Structural insight into the SAM-mediated assembly of the mitochondrial TOM core complex. Wang, Q., Guan, Z., Qi, L. et al. Science (2021) 373:1377-1381. DOI 10.1126/science.abh0704 · PubMed

Other PDB entries of the same protein (UniProt P53969 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7E4H 3.01 Å, Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom
7VKU 3.2 Å, Cryo-EM structure of SAM-Tom40 intermediate complex

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