6N3Q: Yeast Sec complex
Cryo-EM structure of the yeast Sec complex. Determined by electron microscopy at 3.68 Å resolution. Released 19 Dec 2018.
- Method
- Electron microscopy
- Resolution
- 3.68 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 6
- Atoms
- 9,931
- Mol. weight
- 191.99 kDa
- Released
- 19 Dec 2018
Explore 6N3Q in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6N3Q contains 64 α-helices and 27 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: 15 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 1 |
| α-helix | 21-23 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 29-47 | 19 | |
| α-helix | 83-98 | 16 | |
| α-helix | 108-136 | 29 | |
| α-helix | 148-172 | 25 | |
| α-helix | 180-198 | 19 | |
| β-strand | 202-204 | 3 | 2 |
| β-strand | 209-211 | 3 | 2 |
| α-helix | 214-223 | 10 | |
| α-helix | 228-236 | 9 | |
| α-helix | 244-260 | 17 | |
| β-strand | 267-271 | 5 | 3 |
| β-strand | 278-281 | 4 | 3 |
| α-helix | 292-309 | 18 | |
| α-helix | 361-384 | 24 | |
| α-helix | 388-398 | 11 | |
| β-strand | 400-402 | 3 | 3 |
| 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 | 54-81 | 28 | |
Chain C: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-37 | 11 | |
| α-helix | 41-43 | 3 | |
| α-helix | 44-50 | 7 | |
| α-helix | 51-55 | 5 | |
| α-helix | 56-78 | 23 | |
Chain D: 29 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-35 | 22 | |
| α-helix | 55-57 | 3 | |
| α-helix | 59-66 | 8 | |
| α-helix | 69-77 | 9 | |
| α-helix | 94-112 | 19 | |
| β-strand | 205-207 | 3 | 2 |
| α-helix | 219-229 | 11 | |
| α-helix | 230-234 | 5 | |
| α-helix | 235-248 | 14 | |
| α-helix | 256-267 | 12 | |
| α-helix | 274-275 | 2 | |
| α-helix | 279-284 | 6 | |
| α-helix | 288-293 | 6 | |
| α-helix | 299-310 | 12 | |
| α-helix | 319-342 | 24 | |
| α-helix | 346-361 | 16 | |
| α-helix | 369-371 | 3 | |
| α-helix | 379-385 | 7 | |
| α-helix | 392-395 | 4 | |
| α-helix | 402-407 | 6 | |
| α-helix | 412-423 | 12 | |
| β-strand | 427 | 1 | 4 |
| β-strand | 430-436 | 7 | 5 |
| β-strand | 437 | 1 | 6 |
| β-strand | 440 | 1 | 6 |
| β-strand | 450-455 | 6 | 5 |
| β-strand | 458 | 1 | 4 |
| α-helix | 477-478 | 2 | |
| α-helix | 481-484 | 4 | |
| α-helix | 488-492 | 5 | |
| α-helix | 495 | 1 | |
| β-strand | 496 | 1 | 7 |
| α-helix | 497 | 1 | |
| β-strand | 499 | 1 | 8 |
| β-strand | 510 | 1 | 8 |
| β-strand | 513-516 | 4 | 9 |
| β-strand | 519 | 1 | 9 |
| β-strand | 524 | 1 | 9 |
| α-helix | 528-529 | 2 | |
| β-strand | 530-532 | 3 | 9 |
| β-strand | 534 | 1 | 7 |
| α-helix | 542-544 | 3 | |
| α-helix | 567-569 | 3 | |
| β-strand | 571-574 | 4 | 5 |
| α-helix | 578-580 | 3 | |
| β-strand | 584-594 | 11 | 9 |
| β-strand | 602-610 | 9 | 9 |
Chain E: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-85 | 14 | |
| α-helix | 89-123 | 35 | |
| α-helix | 128-155 | 28 | |
| α-helix | 162-181 | 20 | |
| α-helix | 183-194 | 12 | |
Chain F: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 10 |
| β-strand | 12 | 1 | 10 |
| α-helix | 22-41 | 20 | |
| α-helix | 50-51 | 2 | |
| α-helix | 52-70 | 19 | |
| α-helix | 74-90 | 17 | |
| α-helix | 98-119 | 22 | |
| α-helix | 122-135 | 14 | |
| α-helix | 140-152 | 13 | |
| α-helix | 156-167 | 12 | |
| α-helix | 174-191 | 18 | |
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 SSS1 | C | protein | 80 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P35179 (AlphaFold model) |
| Protein transport protein SBH1 | B | protein | 82 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P52870 (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 |
Sequence of entity 1 (A), FASTA
>6N3Q_1 Protein transport protein SEC61 (chains A)
MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETS
DPLYWLRAMLASNRGTLLELGVSPIITSSMIFQFLQGTQLLQIRPESKQDRELFQIAQKV
CAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSG
ISLFTATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN
LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIMLQSALT
SNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPI
KTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPT
AAAFGGATIGALSVGSDLLGTLGSGASILMATTTIYGYYEAAAKEGGFTKNLVPGFSDLM
Sequence of entity 2 (C), FASTA
>6N3Q_2 Protein transport protein SSS1 (chains C)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV
Sequence of entity 3 (B), FASTA
>6N3Q_3 Protein transport protein SBH1 (chains B)
MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFL
AVGFIFSVVALHVISKVAGKLF
Sequence of entity 4 (D), FASTA
>6N3Q_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
>6N3Q_5 Translocation protein SEC66 (chains E)
MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKIS
EQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLL
YKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRY
QSILKRKEVCIKEWELKINNDGRLVN
Sequence of entity 6 (F), FASTA
>6N3Q_6 Translocation protein SEC72 (chains F)
MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKG
LFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILG
KHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALL
IETARNLAEYNGE
Primary citation
Structure of the posttranslational Sec protein-translocation channel complex from yeast. Itskanov, S., Park, E. Science (2019) 363:84-87. DOI 10.1126/science.aav6740 · 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,…
- 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…
- 7AFT 4.4 Å, Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon
Browse structure collections
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