8YA0: Protein translocase subunit SecA

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C). Determined by electron microscopy at 2.97 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Lama glama
Chains: 7
Atoms: 13,920
Mol. weight: 200.4 kDa
Ligands: BEF, MG, ADP
Released: 26 Feb 2025

Explore 8YA0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YA0 contains 69 α-helices and 69 β-strands across 7 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: 42 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	15-32	18
α-helix	43-54	12
α-helix	62-76	15
α-helix	83-93	11
β-strand	97-99	3	1
α-helix	100-101	2
α-helix	106-117	12
β-strand	124-128	5	1
α-helix	131-148	18
β-strand	152-154	3	1
α-helix	161-168	8
β-strand	172-176	5	1
α-helix	177-187	11
α-helix	193-195	3
β-strand	203-207	5	1
α-helix	209	1
α-helix	210-215	6
α-helix	216-218	3
β-strand	220-226	7	2
α-helix	232-241	10
α-helix	245-249	5
β-strand	250-253	4	3
β-strand	258-261	4	3
α-helix	263-272	10
α-helix	284-294	11
α-helix	295-299	5
α-helix	302-305	4
β-strand	306-309	4	4
β-strand	312-316	5	4
α-helix	317	1
β-strand	323-324	2	4
β-strand	327-329	3	2
α-helix	333-341	9
β-strand	349-356	8	2
α-helix	357-361	5
β-strand	367-371	5	1
α-helix	375-377	3
α-helix	378-383	6
β-strand	389-391	3	1
β-strand	400-402	3	5
α-helix	403-405	3
β-strand	406-408	3	6
α-helix	411-426	16
β-strand	432-435	4	5
α-helix	439-450	12
β-strand	456-459	4	5
α-helix	464-466	3
α-helix	467-473	7
β-strand	480-483	4	5
α-helix	493-495	3
α-helix	499-501	3
β-strand	506-509	4	5
α-helix	516-527	12
β-strand	533-537	5	5
β-strand	538-540	3	6
α-helix	544-549	6
α-helix	554-556	3
α-helix	573-618	46
α-helix	624-641	18
α-helix	654-664	11
α-helix	673-675	3
α-helix	681-703	23
α-helix	706-741	36
α-helix	742-744	3
α-helix	748-776	29

Chain B: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-19	17
α-helix	20-23	4
α-helix	37-42	6
α-helix	46-50	5
β-strand	64-67	4	2

Chain C: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	21-23	3	15
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	46-51	6	16
β-strand	57-59	3	16
β-strand	70-72	3	15
β-strand	77-79	3	15
α-helix	84-86	3
β-strand	88-94	7	16
β-strand	102-103	2	16
β-strand	107-109	3	16

Chain E: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	18-19	2	9
α-helix	23-58	36

Chain G: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	17
β-strand	25-36	12	17
β-strand	41-48	8	17
α-helix	58-61	4
β-strand	92-100	9	17
β-strand	105-115	11	17
β-strand	118-128	11	17
β-strand	141	1	18
β-strand	148-155	8	17
β-strand	160-170	11	17
β-strand	171	1	18
β-strand	176-187	12	17
β-strand	199-208	10	17
β-strand	217-227	11	17

Chain V: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	12	1	12
β-strand	17-24	8	11
β-strand	33-37	5	13
β-strand	47-52	6	13
β-strand	58	1	13
β-strand	67-72	6	11
β-strand	77-83	7	11
α-helix	87-89	3
β-strand	91-93	3	14
β-strand	94-98	5	13
β-strand	106	1	13
β-strand	111-113	3	14
β-strand	115	1	12

Chain Y: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	12-32	21
β-strand	35	1	7
α-helix	36	1
α-helix	41-46	6
β-strand	57-60	4	8
β-strand	63-66	4	8
β-strand	68	1	7
α-helix	75-88	14
α-helix	93-101	9
α-helix	105-136	32
α-helix	146-172	27
α-helix	178-201	24
α-helix	213-235	23
β-strand	238-242	5	9
β-strand	244-245	2	10
β-strand	261-265	5	9
α-helix	272-289	18
α-helix	295-303	9
α-helix	309-330	22
α-helix	333-343	11
β-strand	345-346	2	10
α-helix	354-387	34
α-helix	400-420	21
α-helix	421-423	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein translocase subunit SecA	A	protein	765	Bacillus subtilis subsp. subtilis str. 168	P28366 (AlphaFold model)
Protein translocase subunit SecY	Y	protein	429	Geobacillus thermodenitrificans NG80-2	A4IJK8 (AlphaFold model)
Protein translocase subunit SecE	E	protein	58	Geobacillus thermodenitrificans NG80-2	A4IJH4 (AlphaFold model)
Nanobody	V	protein	116	Lama glama
Cell division protein FtsQ,Lactose permease	B	protein	72	Escherichia coli K-12	P02920 (AlphaFold model), Q7CR81
Nanobody	C	protein	113	Lama glama
Green fluorescent protein	G	protein	225	Aequorea victoria	P42212

Sequence of entity 1 (A), FASTA

>8YA0_1 Protein translocase subunit SecA (chains A)
RTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREAS
RRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYL
ASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYK
EQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYD
IKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQV
VIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGT
AKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVL
VGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDI
KLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAER
TMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQ
RFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEK
SDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQ
LRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA

Sequence of entity 2 (Y), FASTA

>8YA0_2 Protein translocase subunit SecY (chains Y)
FRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCG
GALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLG
FIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISI
IIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRKI
PIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIR
RTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVT
RILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLV
KRHYRGFIK

Sequence of entity 3 (E), FASTA

>8YA0_3 Protein translocase subunit SecE (chains E)
QRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVF

Sequence of entity 4 (V), FASTA

>8YA0_4 Nanobody (chains V)
QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKRREVVARIATDDSTMYP
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVS

Sequence of entity 5 (B), FASTA

>8YA0_5 Cell division protein FtsQ,Lactose permease (chains B)
AKKTILFLLTVLTTVLVSGWVVLGAQYEDGCSGVVILKTLHMFEVPFLLVGAFSNADTSI
SGDGDSPHSYHS

Sequence of entity 6 (C), FASTA

>8YA0_6 Nanobody (chains C)
VALVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYE
DSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVS

Sequence of entity 7 (G), FASTA

>8YA0_7 Green fluorescent protein (chains G)
KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVT
TFXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIE
LKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQ
NTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	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
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.…
8Y9Y 3.29 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)
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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