8Y9Y: Protein translocase subunit SecA

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C). Determined by electron microscopy at 3.29 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Escherichia coli K-12
Chains: 4
Atoms: 10,207
Mol. weight: 152.75 kDa
Ligands: MG, ADP, BEF
Released: 26 Feb 2025

Explore 8Y9Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y9Y contains 62 α-helices and 33 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: 40 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	16-33	18
α-helix	36-37	2
α-helix	42-54	13
α-helix	60-77	18
α-helix	83-93	11
β-strand	97-99	3	1
α-helix	112-116	5
β-strand	124-128	5	2
α-helix	131-147	17
β-strand	152-154	3	2
α-helix	161-167	7
β-strand	172-176	5	2
α-helix	177-187	11
α-helix	193-195	3
α-helix	198-201	4
β-strand	203-206	4	2
β-strand	207	1	1
α-helix	209	1
α-helix	210-215	6
α-helix	216-218	3
β-strand	220-226	7	3
α-helix	232-241	10
β-strand	250-253	4	4
β-strand	258-261	4	4
α-helix	263-272	10
α-helix	284-298	15
α-helix	302-305	4
β-strand	307-308	2	5
β-strand	313-314	2	5
β-strand	315-316	2	6
α-helix	317	1
β-strand	323-324	2	6
β-strand	327-329	3	3
α-helix	334-340	7
α-helix	343-345	3
β-strand	349-356	8	3
α-helix	357-361	5
β-strand	367	1	2
β-strand	369-371	3	1
α-helix	375-377	3
α-helix	378-383	6
β-strand	389-391	3	1
β-strand	400-402	3	7
β-strand	406-408	3	8
α-helix	411-426	16
β-strand	432-435	4	7
α-helix	439-450	12
β-strand	456-459	4	7
α-helix	467-471	5
β-strand	480-483	4	7
α-helix	485-488	4
α-helix	500-502	3
β-strand	506-509	4	7
α-helix	516-527	12
β-strand	533-537	5	7
β-strand	538-540	3	8
α-helix	544-549	6
α-helix	555-561	7
β-strand	569	1	8
α-helix	572-618	47
α-helix	624-641	18
α-helix	654-664	11
α-helix	673-675	3
α-helix	681-703	23
α-helix	705-737	33
α-helix	740-742	3
α-helix	748-776	29

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	37-42	6
α-helix	46-50	5
β-strand	64-66	3	3

Chain E: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-17	14
β-strand	19	1	9
α-helix	23-58	36

Chain Y: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	12-30	19
α-helix	35-36	2
α-helix	43-45	3
α-helix	75-88	14
α-helix	93-101	9
α-helix	103-136	34
α-helix	146-173	28
α-helix	178-201	24
α-helix	215-235	21
β-strand	238-242	5	9
β-strand	244	1	10
β-strand	261-265	5	9
α-helix	272-291	20
α-helix	296-303	8
α-helix	309-330	22
α-helix	333-342	10
β-strand	346	1	10
α-helix	354-379	26
α-helix	381-389	9
α-helix	401-422	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein translocase subunit SecA	A	protein	778	Bacillus subtilis subsp. subtilis str. 168	P28366 (AlphaFold model)
Protein translocase subunit SecY	Y	protein	430	Geobacillus thermodenitrificans NG80-2	A4IJK8 (AlphaFold model)
Protein translocase subunit SecE	E	protein	70	Geobacillus thermodenitrificans NG80-2	A4IJH4 (AlphaFold model)
Substrate FtsQ-LacY(+1C)	B	protein	73	Escherichia coli K-12	P02920 (AlphaFold model), P06136

Sequence of entity 1 (A), FASTA

>8Y9Y_1 Protein translocase subunit SecA (chains A)
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDD
LLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALT
GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNEL
GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF
VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY
FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE
DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV
TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS
MEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDL
INTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAV
DSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA

Sequence of entity 2 (Y), FASTA

>8Y9Y_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRK
IPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWI
RRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYV
TRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQL
VKRHYRGFIK

Sequence of entity 3 (E), FASTA

>8Y9Y_3 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE
GGHHHHHHHH

Sequence of entity 4 (B), FASTA

>8Y9Y_4 Substrate FtsQ-LacY(+1C) (chains B)
MAKKTILFLLTVLTTVLVSGWVVLGCQYEDGSSGVVILKTLHMFEVPFLLVGAFSISGDG
DSPHSYHSGDGDK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
BEF	Beryllium trifluoride ion	Be F3	1

Primary citation

SecY translocon chaperones protein folding during membrane protein insertion. Ou, X., Ma, C., Sun, D. et al. Cell (2025) 188:1912-1924.e13. DOI 10.1016/j.cell.2025.01.037 · PubMed

Other PDB entries of the same protein (UniProt P28366 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TF5 2.18 Å, Crystal structure of SecA in an open conformation from Bacillus Subtilis
3JV2 2.5 Å, Crystal Structure of B. subtilis SecA with bound peptide
1M6N 2.7 Å, Crystal structure of the SecA translocation ATPase from Bacillus subtilis
1TF2 2.9 Å, Crystal structure of SecA:ADP in an open conformation from Bacillus Subtilis
8YA0 2.97 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)
1M74 3.0 Å, Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis
2IBM 3.2 Å, A novel dimer interface and conformational changes revealed by an X-ray structure of B.…
3IQY 3.3 Å, Active site mutants of B. subtilis SecA
7XHB 3.33 Å, Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP
7XHA 3.35 Å, Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.
3IQM 3.4 Å, Active site mutants of B. subtilis SecA
8Y9Z 3.41 Å, Structure of the SecA-SecY complex with the substrate HmBRI-3TM

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