7VKU: SAM-Tom40 intermediate complex

Cryo-EM structure of SAM-Tom40 intermediate complex. Determined by electron microscopy at 3.2 Å resolution. Released 4 Jan 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 4
Atoms: 9,219
Mol. weight: 171.53 kDa
Released: 4 Jan 2023

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

Secondary structure: helices and β-sheets

7VKU contains 41 α-helices and 67 β-strands across 4 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: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	1
α-helix	44-54	11
α-helix	64-74	11
β-strand	113-116	4	1
β-strand	128-130	3	2
β-strand	138-141	4	2
β-strand	144	1	2
β-strand	158-164	7	2
β-strand	171-181	11	2
β-strand	184-196	13	2
β-strand	204-216	13	2
β-strand	235-250	16	2
β-strand	271-285	15	2
β-strand	296-306	11	2
β-strand	310-322	13	2
β-strand	330-342	13	2
α-helix	350-352	3
β-strand	357	1	3
β-strand	359	1	4
β-strand	373	1	4
β-strand	376	1	5
β-strand	381	1	5
β-strand	384	1	3
β-strand	386-395	10	2
β-strand	410-420	11	2
α-helix	429-433	5
β-strand	441-449	9	2
β-strand	454-461	8	2
β-strand	464-466	3	6
β-strand	475-480	6	2

Chain B: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	21-23	3	6
α-helix	33-40	8
β-strand	41-42	2	7
β-strand	45	1	8
β-strand	60-64	5	7
β-strand	67-69	3	9
β-strand	75	1	10
β-strand	76-78	3	9
α-helix	83-93	11
β-strand	97	1	8
α-helix	98-99	2
β-strand	100	1	10
β-strand	115-117	3	7
β-strand	130-133	4	7
β-strand	139-141	3	7
α-helix	143-149	7
α-helix	158-167	10
α-helix	170-177	8
α-helix	178-182	5
α-helix	185-191	7
α-helix	196-197	2
α-helix	204-215	12
α-helix	218-224	7
α-helix	230-233	4
α-helix	235-239	5
α-helix	248-271	24
α-helix	272-274	3
α-helix	286-296	11
α-helix	306-311	6
α-helix	314-324	11

Chain C: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	11	1	12
β-strand	14	1	12
α-helix	20-30	11
α-helix	35-37	3
β-strand	47	1	11
α-helix	52-54	3
β-strand	62-65	4	11
β-strand	69-72	4	11
α-helix	74-83	10
α-helix	102-104	3
α-helix	105-107	3
α-helix	108-117	10
α-helix	118-122	5
α-helix	123-129	7
α-helix	134-136	3
α-helix	137-141	5
α-helix	145-147	3
α-helix	157-169	13
α-helix	215-240	26
α-helix	250-262	13
α-helix	268-279	12
α-helix	281-295	15
β-strand	305	1	11
α-helix	316-323	8

Chain X: 0 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	181	1	13
β-strand	198	1	13
β-strand	210-214	5	14
β-strand	231-235	5	14
β-strand	244-245	2	15
β-strand	248	1	14
β-strand	256-258	3	14
β-strand	259-260	2	15
β-strand	262	1	16
β-strand	268	1	16
β-strand	271	1	2
β-strand	272-274	3	14
β-strand	302-304	3	2
β-strand	307	1	17
β-strand	314	1	17
β-strand	315-319	5	2
β-strand	324-330	7	2
β-strand	337-342	6	2
β-strand	344	1	18
β-strand	351	1	18
β-strand	354	1	2
β-strand	357-358	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sorting assembly machinery 50 kDa subunit	A	protein	484	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	327	Saccharomyces cerevisiae S288C	P50110 (AlphaFold model)
Mitochondrial import receptor subunit TOM40	X	protein	387	Saccharomyces cerevisiae S288C	P23644 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7VKU_1 Sorting assembly machinery 50 kDa subunit (chains A)
MTSSSGVDNEISLDSPMPIFNESSTLKPIRVAGVVTTGTDHIDPSVLQAYLDDTIMKSIT
LGQLVKNADVLNKRLCQHHIALNAKQSFHFQGNTYISDEKETHDVVPLMEVVSQLDILPP
KTFTAKTGTNFGNDNDAEAYLQFEKLIDKKYLKLPTRVNLEILRGTKIHSSFLFNSYSSL
SPQSILNLKVFSQFYNWNTNKGLDIGQRGARLSLRYEPLFLHKLLHNPHSNESPTLFHEW
FLETCWRSTKICSQGTSAPYMYSGTMLSQAGDQLRTILGHTFVLDKRDHIMCPTKGSMLK
WSNELSPGKHLKTQLELNSVKSWMNDDFITFSTTIKTGYLKNLSSQQSLPVHICDKFQSG
GPSDIRGFQTFGLGPRDLYDAVGGDAFVSYGLSVFSRLPWKKVEKSNFRLHWFFNGGKLV
NHDNTSLGNCIGQLSKEHSTSTGIGLVLRHPMARFELNFTLPITAHENDLIRKGFQFGLG
LAFL

Sequence of entity 2 (B), FASTA

>7VKU_2 Sorting assembly machinery 35 kDa subunit (chains B)
MVSSFSVPMPVKRIFDTFPLQTYAAQTDKDEAVALEIQRRSYTFTERGGGSSELTVEGTY
KLGVYNVFLEANTGAALATDPWCLFVQLALCQKNGLVLPTHSQEQTPSHTCNHEMLVLSR
LSNPDEALPILVEGYKKRIIRSTVAISEIMRSRILDDAEQLMYYTLLDTVLYDCWITQII
FCASDAQFMELYSCQKLSGSIVTPLDVENSLLQKLSAKSLKISLTKRNKFQFRHREIVKS
MQGVYHNHHNSVNQEQVLNVLFENSKQVLLGLKDMLKSDGQPTYLHLKIASYILCITNVK
EPIKLKTFVENECKELVQFAQDTLKNFVQ

Sequence of entity 3 (C), FASTA

>7VKU_3 Sorting assembly machinery 37 kDa subunit (chains C)
MVKGSVHLWGKDGKASLISVDSIALVWFIKLCTSEEAKSMVAGLQIVFSNNTDLSSDGKL
PVLILDNGTKVSGYVNIVQFLHKNICTSKYEKGTDYEEDLAIVRKKDRLLEYSLLNYVDV
EISRLTDYQLFLNTKNYNEYTKKLFSKLLYFPMWYNTPLQLRSQARENCEEIIGSLTLED
DEEFVESKAMESASQLAQSKTFKIAHKNKIKGKQELQQVKYNLQFDNRLQSCVSNWLAAR
KKLDDSVILSSDLLFLANLYVQLGLPDGNRIRSKLEQTFGSELLNSMSNKIDDFVHRPSN
NLEQRDPQFREQGNVVMSLYNLACKYI

Sequence of entity 4 (X), FASTA

>7VKU_4 Mitochondrial import receptor subunit TOM40 (chains X)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL

Primary citation

Author Correction: A multipoint guidance mechanism for beta-barrel folding on the SAM complex. Takeda, H., Busto, J.V., Lindau, C. et al. Nat Struct Mol Biol (2023) 30:233-233. DOI 10.1038/s41594-023-00926-8 · 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
7E4I 3.05 Å, Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom

Browse structure collections

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