8YA3: Protein translocase subunit SecY

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT. Determined by electron microscopy at 3.27 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.27 Å
Organisms: Geobacillus thermodenitrificans NG80-2, Escherichia coli K-12
Chains: 3
Atoms: 4,060
Mol. weight: 64.03 kDa
Released: 26 Feb 2025

Explore 8YA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YA3 contains 19 α-helices and 11 β-strands across 3 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 B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-18	15
α-helix	37-40	4
α-helix	46-50	5

Chain E: 2 helices, 1 β-strand

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

Chain Y: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	12-32	21
β-strand	35	1	1
β-strand	39	1	2
β-strand	68	1	1
α-helix	75-87	13
α-helix	93-99	7
α-helix	103-133	31
β-strand	141	1	2
α-helix	146-172	27
α-helix	178-201	24
α-helix	213-235	23
β-strand	238-242	5	3
β-strand	244	1	4
β-strand	261-265	5	3
α-helix	272-291	20
α-helix	295-303	9
α-helix	311-330	20
α-helix	333-342	10
β-strand	346	1	4
β-strand	347	1	5
β-strand	350	1	5
α-helix	354-389	36
α-helix	400-421	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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)
Cell division protein FtsQ,Lactose permease	B	protein	78	Escherichia coli K-12	P02920 (AlphaFold model), P06136 (AlphaFold model)

Sequence of entity 1 (Y), FASTA

>8YA3_1 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRK
IPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWI
RRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYV
TRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQL
VKRHYRGFIK

Sequence of entity 2 (E), FASTA

>8YA3_2 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE
GGHHHHHHHH

Sequence of entity 3 (B), FASTA

>8YA3_3 Cell division protein FtsQ,Lactose permease (chains B)
MAKKTILFLLTVLTTVLVSGWVVLGAQYEDGCSGVVILKTLHMFEVPFLLVGAFSISGDG
DSPHSYHSGDGDKLPEGV

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 A4IJK8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YA0 2.97 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)
8Y9Y 3.29 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)
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-.
8Y9Z 3.41 Å, Structure of the SecA-SecY complex with the substrate HmBRI-3TM
6ITC 3.45 Å, Structure of a substrate engaged SecA-SecY protein translocation machine
5EUL 3.7 Å, Structure of the SecA-SecY complex with a translocating polypeptide substrate
8YA2 3.84 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C)
8YAS 3.97 Å, Structure of the SecA-SecY complex with the substrate HmBRI-7TM

Browse structure collections

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