7AFT: Protein transport protein SEC61
Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon. Determined by electron microscopy at 4.4 Å resolution. Released 2 Dec 2020.
- Method
- Electron microscopy
- Resolution
- 4.4 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 8
- Atoms
- 6,691
- Mol. weight
- 247.4 kDa
- Released
- 2 Dec 2020
Explore 7AFT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7AFT contains 59 α-helices and 31 β-strands across 8 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: 17 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 1 |
| α-helix | 21-22 | 2 | |
| α-helix | 29-47 | 19 | |
| α-helix | 83-97 | 15 | |
| α-helix | 109-136 | 28 | |
| α-helix | 149-170 | 22 | |
| α-helix | 171-175 | 5 | |
| α-helix | 180-198 | 19 | |
| β-strand | 202-204 | 3 | 2 |
| β-strand | 209-211 | 3 | 2 |
| α-helix | 214-224 | 11 | |
| α-helix | 228-236 | 9 | |
| α-helix | 244-260 | 17 | |
| β-strand | 265 | 1 | 3 |
| β-strand | 268-271 | 4 | 4 |
| β-strand | 275 | 1 | 5 |
| β-strand | 278-280 | 3 | 4 |
| β-strand | 283 | 1 | 3 |
| α-helix | 291-300 | 10 | |
| α-helix | 301-305 | 5 | |
| α-helix | 306-309 | 4 | |
| α-helix | 361-383 | 23 | |
| α-helix | 388-398 | 11 | |
| β-strand | 400-402 | 3 | 4 |
| α-helix | 409-439 | 31 | |
| α-helix | 445-465 | 21 | |
Chain B: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 52 | 1 | 1 |
| α-helix | 54-80 | 27 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-36 | 9 | |
| α-helix | 44-79 | 36 | |
Chain D: 24 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 2 |
| α-helix | 16-33 | 18 | |
| α-helix | 63-65 | 3 | |
| α-helix | 69-77 | 9 | |
| α-helix | 95-112 | 18 | |
| β-strand | 207 | 1 | 2 |
| α-helix | 212-216 | 5 | |
| α-helix | 219-229 | 11 | |
| α-helix | 230-234 | 5 | |
| α-helix | 235-248 | 14 | |
| β-strand | 249 | 1 | 6 |
| β-strand | 255 | 1 | 6 |
| α-helix | 256-267 | 12 | |
| α-helix | 277-283 | 7 | |
| α-helix | 284-286 | 3 | |
| α-helix | 288-293 | 6 | |
| α-helix | 299-310 | 12 | |
| α-helix | 319-342 | 24 | |
| α-helix | 346-361 | 16 | |
| α-helix | 379-385 | 7 | |
| α-helix | 392-397 | 6 | |
| α-helix | 400-407 | 8 | |
| α-helix | 412-423 | 12 | |
| β-strand | 428-429 | 2 | 7 |
| β-strand | 433-436 | 4 | 8 |
| β-strand | 447 | 1 | 5 |
| β-strand | 450-455 | 6 | 8 |
| β-strand | 456-457 | 2 | 7 |
| α-helix | 467-469 | 3 | |
| α-helix | 481-485 | 5 | |
| α-helix | 489-493 | 5 | |
| β-strand | 496 | 1 | 9 |
| β-strand | 499 | 1 | 10 |
| β-strand | 510 | 1 | 10 |
| β-strand | 513-519 | 7 | 11 |
| β-strand | 525 | 1 | 11 |
| β-strand | 530-532 | 3 | 11 |
| β-strand | 534 | 1 | 9 |
| α-helix | 538-540 | 3 | |
| α-helix | 542-544 | 3 | |
| β-strand | 569-574 | 6 | 8 |
| β-strand | 585-594 | 10 | 11 |
| β-strand | 602-609 | 8 | 11 |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-82 | 11 | |
| α-helix | 89-123 | 35 | |
| α-helix | 129-155 | 27 | |
| α-helix | 163-194 | 32 | |
Chain F: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 12 |
| β-strand | 12 | 1 | 12 |
| α-helix | 22-41 | 20 | |
| α-helix | 52-70 | 19 | |
| α-helix | 74-90 | 17 | |
| α-helix | 98-119 | 22 | |
| α-helix | 123-135 | 13 | |
| α-helix | 140-152 | 13 | |
| α-helix | 157-167 | 11 | |
| α-helix | 175-191 | 17 | |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 152-171 | 20 | |
| α-helix | 184-208 | 25 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-9 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Protein transport protein SEC61 | A | protein | 480 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32915 (AlphaFold model) |
| Protein transport protein SBH1 | B | protein | 82 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P52870 (AlphaFold model) |
| Protein transport protein SSS1 | C | protein | 80 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P35179 (AlphaFold model) |
| Protein translocation protein SEC63 | D | protein | 663 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P14906 (AlphaFold model) |
| Translocation protein SEC66 | E | protein | 206 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33754 |
| Translocation protein SEC72 | F | protein | 193 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P39742 |
| Translocation protein SEC62,Translocation protein SEC62 | G | protein | 324 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P21825 |
| Mating factor alpha-1,Mating factor alpha-1 | H | protein | 178 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P01149 |
Sequence of entity 1 (A), FASTA
>7AFT_1 Protein transport protein SEC61 (chains A)
MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETS
DPLYWLRAMLASNRGTLLELGVSPIITSSMIFQFLQGTQLLQIRPESKQDRELFQIAQKV
CAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSG
ISLFTATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN
LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIMLQSALT
SNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPI
KTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPT
AAAFGGATIGALSVGSDLLGTLGSGASILMATTTIYGYYEAAAKEGGFTKNLVPGFSDLM
Sequence of entity 2 (B), FASTA
>7AFT_2 Protein transport protein SBH1 (chains B)
MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFL
AVGFIFSVVALHVISKVAGKLF
Sequence of entity 3 (C), FASTA
>7AFT_3 Protein transport protein SSS1 (chains C)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV
Sequence of entity 4 (D), FASTA
>7AFT_4 Protein translocation protein SEC63 (chains D)
MPTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDGNSGKSKEFNEEVFK
NLNEEYTSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAILLQRINSNDAIKDAA
TKLFDPYEILGISTSASDRDIKSAYRKLSVKFHPDKLAKGLTPDEKSVMEETYVQITKAY
ESLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVCYVALLGLILPYFVS
RWWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSFAHEFKQFFPDLQPT
DFEKLLQDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNLDIALGAINTFKCIV
QAVPLTPNCQILQLPNVDKEHFITKTGDIHTLGKLFTLEDAKIGEVLGIKDQAKLNETLR
VASHIPNLKIIKADFLVPGENQVTPSSTPYISLKVLVRSAKQPLIPTSLIPEENLTEPQD
FESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKILQTPIIIEKLSYKNL
NDDKDFFDKRIKMDLTKHEKFDINDWEIGTIKIPLGQPAPETVGDFFFRVIVKSTDYFTT
DLDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDDETESDDESDASDYTDIDTDTEAEDDE
SPE
Sequence of entity 5 (E), FASTA
>7AFT_5 Translocation protein SEC66 (chains E)
MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKIS
EQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLL
YKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRY
QSILKRKEVCIKEWELKINNDGRLVN
Sequence of entity 6 (F), FASTA
>7AFT_6 Translocation protein SEC72 (chains F)
MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKG
LFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILG
KHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALL
IETARNLAEYNGE
Sequence of entity 7 (G), FASTA
>7AFT_7 Translocation protein SEC62,Translocation protein SEC62 (chains G)
MSAVGPGSNAGASVNGGSATAIATLLRNHKELKQRQGLFQAKQTDFFRYKRFVRALHSEE
YANKSARQPEIYPTIPSNKIEDQLKSREIFIQLIKAQMVIPVKKLHSQECKEHGLKPSKD
FPHLIVSNKAQLEADEYFVWNYNPRTYMDYLIVIGVVSIILALVCYPLWPRSMRRGSYYV
SLGAFGILAGFFAVAILRLILYVLSLIVYKDVGGFWIFPNLFEDCGVLESFKPLYGFGEK
DTYSYKKKLKRMKKKQAKRESNKKKAINEKAEQNXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 8 (H), FASTA
>7AFT_8 Mating factor alpha-1,Mating factor alpha-1 (chains H)
MRFPSIFTAVLFAASSALAAPVNTTTEDETAQIPAEAVIGYLDLEGDFDVAVLPFSNSTN
NGLLFINTTIASIAAKEEGVSLDKREAEAWHWLQLKPGQPMYKREAEAEAWHWLQLKPGQ
PMYKREADAEAWHWLQLKPGQPMYKREADAEAWHWLQLKPGQPMYXXXXXXXXXXXXX
Primary citation
Architecture of the active post-translational Sec translocon. Weng, T.H., Steinchen, W., Beatrix, B. et al. EMBO J (2021) 40:e105643-e105643. DOI 10.15252/embj.2020105643 · PubMed
Other PDB entries of the same protein (UniProt P32915 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7KAH 3.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class without Sec62
- 7KAJ 3.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62,…
- 7KAI 3.2 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62,…
- 6N3Q 3.68 Å, Cryo-EM structure of the yeast Sec complex
- 7KB5 3.8 Å, Cryo-EM structure of the Sec complex from yeast, Sec63 FN3 and residues 210-216 mutated
- 7KAS 3.9 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class with…
- 7KAO 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class…
- 7KAQ 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
- 7KAR 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class without…
- 7KAU 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3…
- 6ND1 4.1 Å, CryoEM structure of the Sec Complex from yeast
- 7KAP 4.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
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