7KAP: Protein transport protein SEC61
Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with Sec62, conformation 1 (C1). Determined by electron microscopy at 4.1 Å resolution. Released 6 Jan 2021.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organism
- Saccharomyces cerevisiae BY4741
- Chains
- 7
- Atoms
- 10,715
- Mol. weight
- 199.23 kDa
- Released
- 6 Jan 2021
Explore 7KAP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7KAP contains 71 α-helices and 34 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: 22 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 1 |
| α-helix | 21-23 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 29-46 | 18 | |
| β-strand | 50 | 1 | 2 |
| β-strand | 76 | 1 | 2 |
| α-helix | 83-97 | 15 | |
| α-helix | 110-136 | 27 | |
| α-helix | 148-170 | 23 | |
| α-helix | 171-175 | 5 | |
| α-helix | 181-198 | 18 | |
| β-strand | 202-204 | 3 | 3 |
| β-strand | 209-211 | 3 | 3 |
| α-helix | 214-224 | 11 | |
| α-helix | 228-237 | 10 | |
| α-helix | 244-259 | 16 | |
| β-strand | 264-270 | 7 | 4 |
| β-strand | 278-284 | 7 | 4 |
| α-helix | 291-313 | 23 | |
| α-helix | 320-323 | 4 | |
| β-strand | 326-327 | 2 | 5 |
| β-strand | 337-338 | 2 | 5 |
| α-helix | 342-346 | 5 | |
| α-helix | 348-349 | 2 | |
| α-helix | 352-357 | 6 | |
| α-helix | 359-383 | 25 | |
| α-helix | 388-398 | 11 | |
| β-strand | 401-402 | 2 | 4 |
| α-helix | 407-409 | 3 | |
| α-helix | 410-414 | 5 | |
| α-helix | 418-439 | 22 | |
| α-helix | 445-465 | 21 | |
Chain B: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 52 | 1 | 1 |
| α-helix | 54-81 | 28 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-38 | 12 | |
| α-helix | 44-79 | 36 | |
Chain D: 29 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 6 |
| α-helix | 14-35 | 22 | |
| α-helix | 59-62 | 4 | |
| α-helix | 69-77 | 9 | |
| α-helix | 94-111 | 18 | |
| β-strand | 206-207 | 2 | 3 |
| β-strand | 211 | 1 | 6 |
| α-helix | 213-216 | 4 | |
| α-helix | 220-229 | 10 | |
| α-helix | 230-234 | 5 | |
| α-helix | 235-247 | 13 | |
| β-strand | 249 | 1 | 7 |
| β-strand | 255 | 1 | 7 |
| α-helix | 256-267 | 12 | |
| α-helix | 274-275 | 2 | |
| α-helix | 277-284 | 8 | |
| 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 | 393-396 | 4 | |
| α-helix | 400-407 | 8 | |
| α-helix | 412-421 | 10 | |
| β-strand | 427 | 1 | 8 |
| β-strand | 430-436 | 7 | 9 |
| β-strand | 450-455 | 6 | 9 |
| β-strand | 458 | 1 | 8 |
| α-helix | 464-466 | 3 | |
| α-helix | 467-469 | 3 | |
| α-helix | 481-484 | 4 | |
| α-helix | 491-493 | 3 | |
| α-helix | 495 | 1 | |
| β-strand | 496 | 1 | 10 |
| α-helix | 497 | 1 | |
| β-strand | 499 | 1 | 11 |
| β-strand | 510 | 1 | 11 |
| β-strand | 513-519 | 7 | 12 |
| β-strand | 525 | 1 | 12 |
| α-helix | 528-529 | 2 | |
| β-strand | 530-532 | 3 | 12 |
| β-strand | 534 | 1 | 10 |
| α-helix | 538-540 | 3 | |
| α-helix | 555-557 | 3 | |
| β-strand | 570-574 | 5 | 9 |
| α-helix | 578-580 | 3 | |
| β-strand | 584-594 | 11 | 12 |
| β-strand | 602-610 | 9 | 12 |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-85 | 14 | |
| α-helix | 90-123 | 34 | |
| α-helix | 129-155 | 27 | |
| α-helix | 163-181 | 19 | |
| α-helix | 183-194 | 12 | |
| β-strand | 198 | 1 | 13 |
| α-helix | 200-202 | 3 | |
| β-strand | 204 | 1 | 13 |
Chain F: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-6 | 2 | 14 |
| β-strand | 13-14 | 2 | 14 |
| α-helix | 22-40 | 19 | |
| α-helix | 49-51 | 3 | |
| α-helix | 53-70 | 18 | |
| α-helix | 76-90 | 15 | |
| α-helix | 98-119 | 22 | |
| α-helix | 123-134 | 12 | |
| α-helix | 140-152 | 13 | |
| α-helix | 156-167 | 12 | |
| α-helix | 175-191 | 17 | |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 151-169 | 19 | |
| α-helix | 176-204 | 29 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Protein transport protein SEC61 | A | protein | 480 | Saccharomyces cerevisiae BY4741 | P32915 (AlphaFold model) |
| Protein transport protein SSS1 | C | protein | 80 | Saccharomyces cerevisiae BY4741 | P35179 (AlphaFold model) |
| Protein transport protein SBH1 | B | protein | 82 | Saccharomyces cerevisiae BY4741 | P52870 (AlphaFold model) |
| Protein translocation protein SEC63 | D | protein | 694 | Saccharomyces cerevisiae BY4741 | P14906 (AlphaFold model) |
| Translocation protein SEC66 | E | protein | 206 | Saccharomyces cerevisiae BY4741 | P33754 |
| Translocation protein SEC72 | F | protein | 193 | Saccharomyces cerevisiae BY4741 | P39742 |
| Protein transport protein Sec62 | G | protein | 56 | Saccharomyces cerevisiae BY4741 | |
Sequence of entity 1 (A), FASTA
>7KAP_1 Protein transport protein SEC61 (chains A)
MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETS
DPLYWLRAMLASNRGTLLELGVSPIITSSLIFQFLQGTQLLQIRPESKQDRELFQIAQKV
CAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSG
ISLFIATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN
LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIILQSALT
SNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPI
KTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPT
AAAFGGATIGALSVGSDLLGTLGSGASILLATTTIYGYYEAAAKEGGFTKNLVPGFSDLM
Sequence of entity 2 (C), FASTA
>7KAP_2 Protein transport protein SSS1 (chains C)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV
Sequence of entity 3 (B), FASTA
>7KAP_3 Protein transport protein SBH1 (chains B)
MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFL
AVGFIFSVVALHVISKVAGKLF
Sequence of entity 4 (D), FASTA
>7KAP_4 Protein translocation protein SEC63 (chains D)
GGSGGSGGSGGSGGSPTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDG
NSGKSKEFNEEVFKNLNEEYTSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAIL
LQRINSNDAIKDAATKLFDPYEILGISTSASDRDIKSAYRKLSVKFHPDKLAKGLTPDEK
SVMEETYVQITKAYESLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVC
YVALLGLILPYFVSRWWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSF
AHEFKQFFPDLQPTDFEKLLQDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNL
DIALGAINTFKCIVQAVPLTPNCQILQLPNVDKEHFITKTGDIHTLGKLFTLEDAKIGEV
LGIKDQAKLNETLRVASHIPNLKIIKADFLVPGENQVTPSSTPYISLKVLVRSAKQPLIP
TSLIPEENLTEPQDFESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKIL
QTPIIIEKLSYKNLNDDKDFFDKRIKMDLTKHEKFDINDWEIGTIKIPLGQPAPETVGDF
FFRVIVKSTDYFTTDLDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDDETESDDESDASD
YTDIDTDTEAEDDESPEAGGATTASGTGENLYFQ
Sequence of entity 5 (E), FASTA
>7KAP_5 Translocation protein SEC66 (chains E)
MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKIS
EQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLL
YKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRY
QSILKRKEVCIKEWELKINNDGRLVN
Sequence of entity 6 (F), FASTA
>7KAP_6 Translocation protein SEC72 (chains F)
MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKG
LFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILG
KHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALL
IETARNLAEYNGE
Sequence of entity 7 (G), FASTA
>7KAP_7 Protein transport protein Sec62 (chains G)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Primary citation
Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Itskanov, S., Kuo, K.M., Gumbart, J.C. et al. Nat Struct Mol Biol (2021) 28:162-172. DOI 10.1038/s41594-020-00541-x · 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
- 7AFT 4.4 Å, Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon
Browse structure collections
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