8Y9Z: SecA-SecY complex with the substrate HmBRI-3TM
Structure of the SecA-SecY complex with the substrate HmBRI-3TM. Determined by electron microscopy at 3.41 Å resolution. Released 26 Feb 2025.
- Method
- Electron microscopy
- Resolution
- 3.41 Å
- Organisms
- Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Lama glama
- Chains
- 5
- Atoms
- 11,061
- Mol. weight
- 169.16 kDa
- Ligands
- MG, BEF, ADP
- Released
- 26 Feb 2025
Explore 8Y9Z in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8Y9Z contains 65 α-helices and 40 β-strands across 5 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: 39 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-27 | 13 | |
| α-helix | 43-54 | 12 | |
| α-helix | 58-61 | 4 | |
| α-helix | 62-76 | 15 | |
| α-helix | 83-93 | 11 | |
| β-strand | 97-99 | 3 | 1 |
| α-helix | 108-110 | 3 | |
| α-helix | 112-116 | 5 | |
| 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 | |
| α-helix | 198-201 | 4 | |
| β-strand | 204-207 | 4 | 1 |
| α-helix | 209-210 | 2 | |
| α-helix | 211-215 | 5 | |
| α-helix | 216-218 | 3 | |
| β-strand | 221-224 | 4 | 2 |
| α-helix | 232-241 | 10 | |
| β-strand | 250-253 | 4 | 3 |
| β-strand | 258-261 | 4 | 3 |
| α-helix | 263-273 | 11 | |
| α-helix | 284-298 | 15 | |
| 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 |
| α-helix | 333-340 | 8 | |
| β-strand | 351-355 | 5 | 2 |
| α-helix | 357-360 | 4 | |
| β-strand | 367-371 | 5 | 1 |
| α-helix | 378-384 | 7 | |
| β-strand | 389-391 | 3 | 1 |
| β-strand | 400-402 | 3 | 5 |
| β-strand | 406-408 | 3 | 6 |
| α-helix | 411-426 | 16 | |
| β-strand | 432-435 | 4 | 5 |
| α-helix | 440-448 | 9 | |
| α-helix | 451-453 | 3 | |
| β-strand | 456-459 | 4 | 5 |
| α-helix | 467-473 | 7 | |
| β-strand | 480-483 | 4 | 5 |
| α-helix | 485-487 | 3 | |
| β-strand | 506-509 | 4 | 5 |
| α-helix | 516-523 | 8 | |
| β-strand | 533-537 | 5 | 5 |
| β-strand | 538-540 | 3 | 6 |
| α-helix | 544-549 | 6 | |
| α-helix | 557-561 | 5 | |
| α-helix | 575-618 | 44 | |
| α-helix | 624-641 | 18 | |
| α-helix | 656-664 | 9 | |
| α-helix | 673-675 | 3 | |
| α-helix | 681-703 | 23 | |
| α-helix | 706-734 | 29 | |
| α-helix | 736-744 | 9 | |
| α-helix | 750-776 | 27 | |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-59 | 25 | |
| α-helix | 73-83 | 11 | |
Chain E: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-14 | 12 | |
| α-helix | 15-17 | 3 | |
| β-strand | 19 | 1 | 7 |
| α-helix | 23-58 | 36 | |
Chain V: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-7 | 3 | 9 |
| β-strand | 11-12 | 2 | 10 |
| β-strand | 17-23 | 7 | 9 |
| β-strand | 33-37 | 5 | 11 |
| β-strand | 47-51 | 5 | 11 |
| β-strand | 58 | 1 | 11 |
| β-strand | 67-71 | 5 | 9 |
| β-strand | 78-83 | 6 | 9 |
| α-helix | 87-89 | 3 | |
| β-strand | 93 | 1 | 12 |
| β-strand | 94-98 | 5 | 11 |
| α-helix | 103-105 | 3 | |
| β-strand | 106 | 1 | 11 |
| β-strand | 111 | 1 | 12 |
| β-strand | 114-115 | 2 | 10 |
Chain Y: 19 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-8 | 6 | |
| α-helix | 12-30 | 19 | |
| α-helix | 31-33 | 3 | |
| α-helix | 34-36 | 3 | |
| α-helix | 75-87 | 13 | |
| α-helix | 93-96 | 4 | |
| α-helix | 103-106 | 4 | |
| α-helix | 110-136 | 27 | |
| α-helix | 146-172 | 27 | |
| α-helix | 178-188 | 11 | |
| α-helix | 191-201 | 11 | |
| α-helix | 213-235 | 23 | |
| β-strand | 238-242 | 5 | 7 |
| β-strand | 244-245 | 2 | 8 |
| β-strand | 261-265 | 5 | 7 |
| α-helix | 272-287 | 16 | |
| α-helix | 295-303 | 9 | |
| α-helix | 309-331 | 23 | |
| α-helix | 333-343 | 11 | |
| β-strand | 345-346 | 2 | 8 |
| α-helix | 354-389 | 36 | |
| α-helix | 400-418 | 19 | |
| α-helix | 421-423 | 3 | |
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) |
| Nanobody | V | protein | 117 | Lama glama | |
| Bacteriorhodopsin-I | B | protein | 99 | Haloarcula marismortui ATCC 43049 | Q5UXY6 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>8Y9Z_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
>8Y9Z_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRK
IPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWI
RRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYV
TRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQL
VKRHYRGFIK
Sequence of entity 3 (E), FASTA
>8Y9Z_3 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE
GGHHHHHHHH
Sequence of entity 4 (V), FASTA
>8Y9Z_4 Nanobody (chains V)
QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKRREVVARIATDDSTMYP
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVSS
Sequence of entity 5 (B), FASTA
>8Y9Z_5 Bacteriorhodopsin-I (chains B)
MPAPGSEGIWLWLGTAGMFLGMLYFIARGWGETDGRRQKFYIATILITAIAFVNYLAMAL
GFGLTFIEFGGEQHCIYWARYTDWLFTTPLLLYDLGLLA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
| BEF | Beryllium trifluoride ion | Be F3 | 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
- 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
About this viewer
MolViewer shows 8Y9Z directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.