6C26: Eukaryotic oligosaccharyl transferase complex
The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex. Determined by electron microscopy at 3.5 Å resolution. Released 31 Jan 2018.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 8
- Atoms
- 17,188
- Mol. weight
- 291.73 kDa
- Ligands
- NAG, EGY
- Released
- 31 Jan 2018
Explore 6C26 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6C26 contains 73 α-helices and 92 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 1: 8 helices, 39 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-41 | 10 | 4 |
| β-strand | 48-56 | 9 | 4 |
| β-strand | 66-70 | 5 | 5 |
| β-strand | 81 | 1 | 4 |
| β-strand | 94-96 | 3 | 5 |
| β-strand | 113-117 | 5 | 5 |
| β-strand | 129-136 | 8 | 4 |
| β-strand | 142-143 | 2 | 6 |
| β-strand | 147 | 1 | 7 |
| β-strand | 154-158 | 5 | 6 |
| β-strand | 161 | 1 | 8 |
| β-strand | 170 | 1 | 4 |
| β-strand | 174-178 | 5 | 4 |
| β-strand | 183-185 | 3 | 6 |
| α-helix | 192-194 | 3 | |
| β-strand | 197-199 | 3 | 4 |
| β-strand | 202-204 | 3 | 4 |
| β-strand | 211 | 1 | 4 |
| β-strand | 219 | 1 | 8 |
| β-strand | 222-226 | 5 | 6 |
| β-strand | 231-242 | 12 | 9 |
| β-strand | 249-252 | 4 | 9 |
| β-strand | 255-259 | 5 | 9 |
| α-helix | 262 | 1 | |
| β-strand | 263 | 1 | 7 |
| α-helix | 264 | 1 | |
| α-helix | 270-278 | 9 | |
| β-strand | 288 | 1 | 10 |
| β-strand | 291-294 | 4 | 11 |
| β-strand | 303-305 | 3 | 9 |
| β-strand | 310 | 1 | 9 |
| β-strand | 314-316 | 3 | 11 |
| β-strand | 320-323 | 4 | 11 |
| β-strand | 329 | 1 | 10 |
| β-strand | 334-342 | 9 | 9 |
| α-helix | 345-347 | 3 | |
| β-strand | 349-351 | 3 | 12 |
| β-strand | 358-364 | 7 | 12 |
| β-strand | 373-383 | 11 | 9 |
| α-helix | 384 | 1 | |
| β-strand | 388-393 | 6 | 12 |
| β-strand | 401-406 | 6 | 9 |
| β-strand | 416-422 | 7 | 9 |
| β-strand | 426-427 | 2 | 9 |
| β-strand | 434-440 | 7 | 12 |
| α-helix | 443-446 | 4 | |
| α-helix | 449-468 | 20 | |
Chain 2: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-40 | 18 | |
| α-helix | 44-67 | 24 | |
| α-helix | 74-99 | 26 | |
| α-helix | 101-102 | 2 | |
| α-helix | 109-124 | 16 | |
Chain 3: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 210-215 | 6 | |
| α-helix | 218-232 | 15 | |
| α-helix | 235-240 | 6 | |
| α-helix | 269-288 | 20 | |
| α-helix | 292-296 | 5 | |
| α-helix | 306-334 | 29 | |
Chain 4: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-31 | 28 | |
Chain 5: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-11 | 9 | |
| β-strand | 14 | 1 | 12 |
| α-helix | 25-45 | 21 | |
| α-helix | 53-79 | 27 | |
Chain A: 38 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-24 | 19 | |
| α-helix | 26-31 | 6 | |
| α-helix | 34-37 | 4 | |
| α-helix | 48-54 | 7 | |
| α-helix | 58-60 | 3 | |
| α-helix | 64-67 | 4 | |
| β-strand | 70-71 | 2 | 1 |
| α-helix | 79 | 1 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 92-103 | 12 | |
| α-helix | 111-116 | 6 | |
| α-helix | 119-137 | 19 | |
| α-helix | 143-149 | 7 | |
| α-helix | 168-187 | 20 | |
| α-helix | 192-205 | 14 | |
| α-helix | 212-215 | 4 | |
| α-helix | 218-227 | 10 | |
| α-helix | 235-250 | 16 | |
| α-helix | 259-262 | 4 | |
| α-helix | 267-281 | 15 | |
| α-helix | 285-287 | 3 | |
| α-helix | 293-296 | 4 | |
| α-helix | 357-362 | 6 | |
| α-helix | 370-378 | 9 | |
| α-helix | 385-398 | 14 | |
| α-helix | 410-416 | 7 | |
| α-helix | 420-428 | 9 | |
| α-helix | 442-472 | 31 | |
| α-helix | 498-505 | 8 | |
| β-strand | 512-514 | 3 | 2 |
| α-helix | 517-519 | 3 | |
| α-helix | 520-522 | 3 | |
| α-helix | 523-527 | 5 | |
| β-strand | 530-531 | 2 | 2 |
| α-helix | 543-549 | 7 | |
| α-helix | 554-562 | 9 | |
| β-strand | 568-572 | 5 | 2 |
| α-helix | 587-593 | 7 | |
| α-helix | 628-631 | 4 | |
| α-helix | 642-644 | 3 | |
| β-strand | 646-647 | 2 | 3 |
| β-strand | 654-655 | 2 | 3 |
| α-helix | 661-663 | 3 | |
| β-strand | 666-671 | 6 | 2 |
| β-strand | 677-682 | 6 | 2 |
| α-helix | 683-686 | 4 | |
| α-helix | 692-700 | 9 | |
Chain B: 7 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25 | 1 | 18 |
| β-strand | 28-29 | 2 | 19 |
| β-strand | 30 | 1 | 20 |
| α-helix | 38-40 | 3 | |
| α-helix | 41-49 | 9 | |
| β-strand | 53 | 1 | 18 |
| β-strand | 58 | 1 | 20 |
| β-strand | 69-70 | 2 | 21 |
| β-strand | 73-74 | 2 | 21 |
| β-strand | 78-81 | 4 | 19 |
| α-helix | 88-93 | 6 | |
| α-helix | 96-103 | 8 | |
| β-strand | 108-112 | 5 | 19 |
| α-helix | 121-129 | 9 | |
| β-strand | 131-133 | 3 | 19 |
| β-strand | 139-142 | 4 | 22 |
| β-strand | 151-154 | 4 | 23 |
| β-strand | 171-174 | 4 | 23 |
| β-strand | 177 | 1 | 24 |
| β-strand | 180-182 | 3 | 19 |
| β-strand | 188-193 | 6 | 19 |
| β-strand | 198-201 | 4 | 22 |
| β-strand | 216-221 | 6 | 19 |
| β-strand | 229-232 | 4 | 19 |
| β-strand | 234 | 1 | 24 |
| α-helix | 247-256 | 10 | |
| β-strand | 263-273 | 11 | 25 |
| β-strand | 289-299 | 11 | 25 |
| β-strand | 304-305 | 2 | 25 |
| β-strand | 313-317 | 5 | 17 |
| β-strand | 321-326 | 6 | 17 |
| β-strand | 328-329 | 2 | 25 |
| β-strand | 337-340 | 4 | 25 |
| β-strand | 344-345 | 2 | 25 |
| β-strand | 351-356 | 6 | 17 |
| β-strand | 359 | 1 | 26 |
| β-strand | 367 | 1 | 26 |
| β-strand | 372-375 | 4 | 17 |
| α-helix | 393-411 | 19 | |
Chain C: 5 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25-27 | 3 | 13 |
| β-strand | 38 | 1 | 14 |
| β-strand | 57 | 1 | 15 |
| β-strand | 71 | 1 | 15 |
| β-strand | 81-87 | 7 | 16 |
| β-strand | 92-96 | 5 | 16 |
| β-strand | 108-110 | 3 | 13 |
| α-helix | 122-126 | 5 | |
| β-strand | 134-139 | 6 | 16 |
| β-strand | 150-155 | 6 | 16 |
| β-strand | 158 | 1 | 14 |
| β-strand | 180 | 1 | 17 |
| α-helix | 186-192 | 7 | |
| α-helix | 196-216 | 21 | |
| α-helix | 231-253 | 23 | |
| α-helix | 257-282 | 26 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 | A | protein | 718 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P39007 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | 1 | protein | 476 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P41543 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 | 5 | protein | 86 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q92316 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 | 4 | protein | 36 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q99380 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 | 2 | protein | 130 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P46964 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 | 3 | protein | 350 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P48439 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 | C | protein | 286 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q02795 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 | B | protein | 430 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33767 |
Sequence of entity 1 (A), FASTA
>6C26_1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (chains A)
MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVN
NSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAP
LFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFM
FWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYT
TWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMV
SLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFF
FDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVA
LSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVV
LPSQTPDGKLALIDDFREAYYWLRMNSDEDSKVAAWWDYGYQIGGMADRTTLVDNNTWNN
THIAIVGKAMASPEEKSYEILKEHDVDYVLVIFGGLIGFGGDDINKFLWMIRISEGIWPE
EIKERDFYTAEGEYRVDARASETMRNSLLYKMSYKDFPQLFNGGQATDRVRQQMITPLDV
PPLDYFDEVFTSENWMVRIYQLKKDDAQGRTLRDVGELTRSSTKTRRSIKRPELGLRV
Sequence of entity 2 (1), FASTA
>6C26_2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (chains 1)
MRQVWFSWIVGLFLCFFNVSSAAQYEPPATWENVDYKRTIDVSNAYISETIEITIKNIAS
EPATEYFTAFESGIFSKVSFFSAYFTNEATFLNSQLLANSTTAPGDDGESEIRYGIIQFP
NAISPQEEVSLVIKSFYNTVGIPYPEHVGMSEEQHLLWETNRLPLSAYDTKKASFTLIGS
SSFEEYHPPNDESLLGKANGNSFEFGPWEDIPRFSSNETLAIVYSHNAPLNQVVNLRRDI
WLSHWASTIQFEEYYELTNKAAKLSKGFSRLELMKQIQTQNMRQTHFVTVLDMLLPEGAT
DHYFTDLVGLVSTSHAERDHFFIRPRFPIFGGWNYNFTVGWTNKLSDFLHVSSGSDEKFV
ASIPILNGPPDTVYDNVELSVFLPEGAEIFDIDSPVPFTNVSIETQKSYFDLNKGHVKLT
FSYRNLISQVANGQVLIKYDYPKSSFFKKPLSIACYIFTALMGVFVLKTLNMNVTN
Sequence of entity 3 (5), FASTA
>6C26_3 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (chains 5)
MTYEQLYKEFHSSKSFQPFIHLDTQPKFAICGLIVTLAVLSSALFAVGSKSSYIKKLFFY
TILSVIGSLFAGLTTVFASNSFGVYV
Sequence of entity 4 (4), FASTA
>6C26_4 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (chains 4)
MISDEQLNSLAITFGIVMMTLIVIYHAVDSTMSPKN
Sequence of entity 5 (2), FASTA
>6C26_5 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (chains 2)
MAKAPKANTPKVTSTSSAVLTDFQETFKTSKRAYFAQIEKYPKLKLIDTFCFFLVLLGVI
QCTFIILIRDNFPFNAFLAGFIICVGQFVLLMSLRLQLCNSFPGISKNRAFAEFIVASLI
LHFVCLHFIN
Sequence of entity 6 (3), FASTA
>6C26_6 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 (chains 3)
MNWLFLVSLVFFCGVSTHPALAMSSNRLLKLANKSPKKIIPLKDSSFENILAPPHENAYI
VALFTATAPEIGCSLCLELESEYDTIVASWFDDHPDAKSSNSDTSIFFTKVNLEDPSKTI
PKAFQFFQLNNVPRLFIFKPNSPSILDHSVISISTDTGSERMKQIIQAIKQFSQVNDFSL
HLPMDWTPIITSTIITFITVLLFKKQSKLMFSIISSRIIWATLSTFFIICMISAYMFNQI
RNTQLAGVGPKGEVMYFLPNEFQHQFAIETQVMVLIYGTLAALVVVLVKGIQFLRSHLYP
ETKKAYFIDAILASFCALFIYVFFAALTTVFTIKSPAYPFPLLRLSAPFK
Sequence of entity 7 (C), FASTA
>6C26_7 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (chains C)
MQFFKTLAALVSCISFVLAYVAQDVHVSFPSTAGKSRVMIGKVEPRIGIDETVPTTITVE
DPNEVIQVNFAIESTNKPFQNTLLIGLPNKNLEMAFEPEIKDNGKLSMYKYRIDLAKLDA
ALLQEASRSPEPIKATLILASSTAKPKENLFREILQLNLNFDVDHSDSSLVDKFGIKPEI
HHIFHAEPKRVAKPIAVIFVLIIFITILSLIVTWLNSCAAAFNNIPTGVTAVYFLGFIAT
IVGFEVIFARYYLGTSIFETLFSSLYLGAPGLLTSTKFLRSFGQTI
Sequence of entity 8 (B), FASTA
>6C26_8 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains B)
MRTDWNFFFCILLQAIFVVGTQTSRTLVLYDQSTEPLEEYSVYLKDLEQRNYKLEYLDIN
STSTTVDLYDKEQRLFDNIIVFPTKGGKNLARQIPVKQLIKFFENEGNILCMSSPGAVPN
TIRLFLNELGIYPSPKGHVIRDYFSPSSEELVVSSNHLLNKYVYNARKSEDFVFGESSAA
LLENREQIVPILNAPRTSFTESKGKCNSWTSGSQGFLVVGFQNLNNARLVWIGSSDFLKN
KNQDSNQEFAKELLKWTFNEKSVIKSVHAVHSHADGTSYDEEPYKIKDKVIYSVGFSEWN
GEEWLPHIADDIQFELRQVDPYYRLTLSPSGNDSETQYYTTGEFILPDRHGVFTFLTDYR
KIGLSFTTDKDVKAIRHLANDEYPRSWEISNSWVYISAICGVIVAWIFFVVSFVTTSSVG
KKLETFKKTN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| EGY | (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-tri… | C33 H67 N O8 P | 8 |
Primary citation
The atomic structure of a eukaryotic oligosaccharyltransferase complex. Bai, L., Wang, T., Zhao, G. et al. Nature (2018) 555:328-333. DOI 10.1038/nature25755 · PubMed
Other PDB entries of the same protein (UniProt P39007 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8AGE 2.8 Å, Structure of yeast oligosaccharylransferase complex with acceptor peptide bound
- 8AGB 3.0 Å, Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide…
- 8AGC 3.1 Å, Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide…
- 6EZN 3.3 Å, Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex
- 7OCI 3.46 Å, Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex
- 2LGZ Solution structure of STT3P
Browse structure collections
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