8YA2: Protein translocase subunit SecA
Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C). Determined by electron microscopy at 3.84 Å resolution. Released 26 Feb 2025.
- Method
- Electron microscopy
- Resolution
- 3.84 Å
- Organisms
- Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Escherichia coli K-12
- Chains
- 6
- Atoms
- 12,899
- Mol. weight
- 191.73 kDa
- Ligands
- ADP, BEF, MG
- Released
- 26 Feb 2025
Explore 8YA2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YA2 contains 65 α-helices and 56 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: 43 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-33 | 19 | |
| α-helix | 40-52 | 13 | |
| α-helix | 62-76 | 15 | |
| α-helix | 83-93 | 11 | |
| β-strand | 97-99 | 3 | 1 |
| α-helix | 106-117 | 12 | |
| β-strand | 124-128 | 5 | 2 |
| α-helix | 131-148 | 18 | |
| β-strand | 152-154 | 3 | 2 |
| α-helix | 161-168 | 8 | |
| β-strand | 172-176 | 5 | 2 |
| α-helix | 177-186 | 10 | |
| β-strand | 203-206 | 4 | 2 |
| α-helix | 209-210 | 2 | |
| α-helix | 211-215 | 5 | |
| α-helix | 220 | 1 | |
| β-strand | 221-226 | 6 | 3 |
| α-helix | 232-242 | 11 | |
| α-helix | 246-248 | 3 | |
| β-strand | 250-253 | 4 | 4 |
| β-strand | 258-261 | 4 | 4 |
| α-helix | 263-273 | 11 | |
| α-helix | 281-283 | 3 | |
| α-helix | 284-298 | 15 | |
| α-helix | 302-305 | 4 | |
| β-strand | 306-309 | 4 | 5 |
| β-strand | 312-315 | 4 | 5 |
| β-strand | 316 | 1 | 6 |
| β-strand | 323 | 1 | 6 |
| α-helix | 333-340 | 8 | |
| α-helix | 347-348 | 2 | |
| β-strand | 349-355 | 7 | 3 |
| α-helix | 357-362 | 6 | |
| β-strand | 367-369 | 3 | 2 |
| β-strand | 371 | 1 | 1 |
| α-helix | 378-383 | 6 | |
| β-strand | 389-391 | 3 | 1 |
| β-strand | 400-402 | 3 | 7 |
| α-helix | 403-405 | 3 | |
| β-strand | 407-408 | 2 | 8 |
| α-helix | 411-426 | 16 | |
| β-strand | 432-435 | 4 | 7 |
| α-helix | 440-448 | 9 | |
| β-strand | 459 | 1 | 7 |
| α-helix | 464-466 | 3 | |
| α-helix | 467-472 | 6 | |
| α-helix | 473-475 | 3 | |
| β-strand | 480-483 | 4 | 7 |
| α-helix | 485-487 | 3 | |
| α-helix | 493-495 | 3 | |
| α-helix | 500-502 | 3 | |
| β-strand | 506-508 | 3 | 7 |
| α-helix | 516-524 | 9 | |
| β-strand | 533-536 | 4 | 7 |
| β-strand | 539-540 | 2 | 8 |
| α-helix | 544-549 | 6 | |
| α-helix | 553-555 | 3 | |
| α-helix | 558-561 | 4 | |
| α-helix | 572-618 | 47 | |
| α-helix | 624-641 | 18 | |
| α-helix | 654-660 | 7 | |
| α-helix | 661-665 | 5 | |
| α-helix | 668-670 | 3 | |
| α-helix | 673-675 | 3 | |
| α-helix | 681-703 | 23 | |
| α-helix | 706-741 | 36 | |
| α-helix | 748-775 | 28 | |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-18 | 16 | |
| α-helix | 37-44 | 8 | |
Chain C: 1 helix, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-7 | 3 | 12 |
| β-strand | 12 | 1 | 13 |
| β-strand | 21-23 | 3 | 12 |
| β-strand | 34-39 | 6 | 14 |
| β-strand | 46-52 | 7 | 14 |
| β-strand | 56-59 | 4 | 14 |
| β-strand | 70-72 | 3 | 12 |
| β-strand | 77-79 | 3 | 12 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-96 | 9 | 14 |
| β-strand | 98-103 | 4 | 14 |
| β-strand | 107-109 | 3 | 14 |
| β-strand | 111 | 1 | 13 |
Chain E: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| β-strand | 19 | 1 | 10 |
| α-helix | 23-57 | 35 | |
Chain G: 1 helix, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-22 | 11 | 15 |
| β-strand | 25-36 | 12 | 15 |
| β-strand | 41-48 | 8 | 15 |
| α-helix | 58-61 | 4 | |
| β-strand | 92-100 | 9 | 15 |
| β-strand | 105-115 | 11 | 15 |
| β-strand | 118-128 | 11 | 15 |
| β-strand | 141 | 1 | 16 |
| β-strand | 148-155 | 8 | 15 |
| β-strand | 160-170 | 11 | 15 |
| β-strand | 171 | 1 | 16 |
| β-strand | 176-187 | 12 | 15 |
| β-strand | 199-208 | 10 | 15 |
| β-strand | 217-227 | 11 | 15 |
Chain Y: 16 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-10 | 8 | |
| α-helix | 12-31 | 20 | |
| β-strand | 35 | 1 | 9 |
| α-helix | 41-49 | 9 | |
| α-helix | 61-65 | 5 | |
| β-strand | 68 | 1 | 9 |
| α-helix | 75-87 | 13 | |
| α-helix | 93-99 | 7 | |
| α-helix | 103-136 | 34 | |
| α-helix | 149-173 | 25 | |
| α-helix | 178-201 | 24 | |
| α-helix | 215-235 | 21 | |
| β-strand | 238-242 | 5 | 10 |
| β-strand | 244 | 1 | 11 |
| β-strand | 261-265 | 5 | 10 |
| α-helix | 272-291 | 20 | |
| α-helix | 295-303 | 9 | |
| α-helix | 312-330 | 19 | |
| α-helix | 333-342 | 10 | |
| β-strand | 346 | 1 | 11 |
| α-helix | 354-388 | 35 | |
| α-helix | 400-423 | 24 | |
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) |
| Cell division protein FtsQ,Lactose permease | B | protein | 83 | Escherichia coli K-12 | P02920 (AlphaFold model), P06136 |
| Nanobody | C | protein | 114 | Lama glama | |
| Green fluorescent protein | G | protein | 225 | Aequorea victoria | P42212 |
Sequence of entity 1 (A), FASTA
>8YA2_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
>8YA2_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRK
IPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWI
RRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYV
TRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQL
VKRHYRGFIK
Sequence of entity 3 (E), FASTA
>8YA2_3 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE
GGHHHHHHHH
Sequence of entity 4 (B), FASTA
>8YA2_4 Cell division protein FtsQ,Lactose permease (chains B)
MAKKTILFLLTVLTTVLVSGWVVLGAQYEDGSSGVVILKTLHMFCVPFLLVGAFSNADTS
ISGDGDSPHSYHSGDGDKLPEGV
Sequence of entity 5 (C), FASTA
>8YA2_5 Nanobody (chains C)
VALVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYE
DSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVSS
Sequence of entity 6 (G), FASTA
>8YA2_6 Green fluorescent protein (chains G)
KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVT
TFXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIE
LKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQ
NTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| MG | Magnesium ion | Mg | 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.…
- 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
Browse structure collections
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