7KAT: Protein transport protein SEC61
Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3 double mutant, class without Sec62. Determined by electron microscopy at 4.4 Å resolution. Released 6 Jan 2021.
- Method
- Electron microscopy
- Resolution
- 4.4 Å
- Organism
- Saccharomyces cerevisiae BY4741
- Chains
- 6
- Atoms
- 10,431
- Mol. weight
- 192.82 kDa
- Released
- 6 Jan 2021
Explore 7KAT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7KAT contains 66 α-helices and 35 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: 21 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 1 |
| α-helix | 21-23 | 3 | |
| α-helix | 29-46 | 18 | |
| β-strand | 50 | 1 | 2 |
| α-helix | 64-69 | 6 | |
| β-strand | 76 | 1 | 2 |
| α-helix | 83-97 | 15 | |
| α-helix | 108-136 | 29 | |
| α-helix | 148-170 | 23 | |
| α-helix | 171-175 | 5 | |
| α-helix | 181-195 | 15 | |
| β-strand | 202-204 | 3 | 3 |
| β-strand | 209-211 | 3 | 3 |
| α-helix | 214-225 | 12 | |
| α-helix | 228-237 | 10 | |
| α-helix | 244-259 | 16 | |
| β-strand | 264-271 | 8 | 4 |
| β-strand | 278-284 | 7 | 4 |
| α-helix | 290-313 | 24 | |
| α-helix | 318-323 | 6 | |
| 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 | 400-402 | 3 | 4 |
| α-helix | 410-415 | 6 | |
| 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, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-38 | 12 | |
| β-strand | 39 | 1 | 4 |
| α-helix | 44-79 | 36 | |
Chain D: 28 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 6 |
| α-helix | 14-35 | 22 | |
| α-helix | 59-66 | 8 | |
| α-helix | 69-77 | 9 | |
| α-helix | 94-112 | 19 | |
| 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 | 235-248 | 14 | |
| 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 | 392-396 | 5 | |
| α-helix | 400-407 | 8 | |
| α-helix | 412-422 | 11 | |
| β-strand | 427 | 1 | 8 |
| β-strand | 430-434 | 5 | 9 |
| β-strand | 450-455 | 6 | 9 |
| β-strand | 458 | 1 | 8 |
| α-helix | 467-469 | 3 | |
| α-helix | 481-485 | 5 | |
| α-helix | 488-491 | 4 | |
| 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 | 161-181 | 21 | |
| α-helix | 183-194 | 12 | |
| β-strand | 198 | 1 | 13 |
| α-helix | 200-202 | 3 | |
| β-strand | 204 | 1 | 13 |
Chain F: 8 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 | 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 | |
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 | 676 | 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 |
Sequence of entity 1 (A), FASTA
>7KAT_1 Protein transport protein SEC61 (chains A)
MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETS
DPLYWLRAMLASNRGTLLELGVSPIITSSLIFQFLQGTQLLQIRPESKQDRELFQIAQKV
CAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSG
ISLFIATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN
LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIILQSALT
SNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPI
KTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPT
AAAFGGATIGALSVGSDLLGTLGSGASILLATTTIYGYYEAAAKEGGFTKNLVPGFSDLM
Sequence of entity 2 (C), FASTA
>7KAT_2 Protein transport protein SSS1 (chains C)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV
Sequence of entity 3 (B), FASTA
>7KAT_3 Protein transport protein SBH1 (chains B)
MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFL
AVGFIFSVVALHVISKVAGKLF
Sequence of entity 4 (D), FASTA
>7KAT_4 Protein translocation protein SEC63 (chains D)
GGSGGSGGSGGSGGSPTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDG
NSGKSKEFNEEVFKNLNEEYTSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAIL
LQRINSNDAIKDAATKLFDPYEILGISTSASDRDIKSAYRKLSVKFHPDKLAKGLTPDEK
SVMEETYVQITKAYESLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVC
YVALLGLILPYFVSRWWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSF
AHEFKQFFPDLQPTDFEKLLQDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNL
DIALGAINTFKCIVQAVPLTPNCQILQLPNVDKEHFITKTGDIHTLGKLFTLEDAKIGEV
LGIKDQAKLNETLRVASHIPNLKIIKADFLVPGRPYISLKVLVRSAKQPLIPTSLIPEEN
LTEPQDSESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKILQTPIIIEK
LSYKNLNDDKDFFDKRIKMDLTKHEKFDINDWEIGTIKIPLGQPAPETVGDFFFRVIVKS
TDYFTTDLDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDDETESDDESDASDYTDIDTDT
EAEDDESPEGENLYFQ
Sequence of entity 5 (E), FASTA
>7KAT_5 Translocation protein SEC66 (chains E)
MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKIS
EQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLL
YKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRY
QSILKRKEVCIKEWELKINNDGRLVN
Sequence of entity 6 (F), FASTA
>7KAT_6 Translocation protein SEC72 (chains F)
MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKG
LFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILG
KHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALL
IETARNLAEYNGE
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
- 7KAP 4.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
Browse structure collections
About this viewer
MolViewer shows 7KAT 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.