7OCI: PDB entry 7OCI
Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex. Determined by electron microscopy at 3.46 Å resolution. Released 16 Feb 2022.
- Method
- Electron microscopy
- Resolution
- 3.46 Å
- Organism
- Saccharomyces cerevisiae S288C
- Chains
- 9
- Atoms
- 17,077
- Mol. weight
- 295.17 kDa
- Ligands
- PEE, NAG, AJP, MG
- Released
- 16 Feb 2022
Explore 7OCI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7OCI contains 83 α-helices and 100 β-strands across 9 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: 11 helices, 40 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-41 | 11 | 1 |
| β-strand | 48-57 | 10 | 1 |
| β-strand | 66-70 | 5 | 2 |
| α-helix | 72-75 | 4 | |
| β-strand | 78-84 | 7 | 1 |
| β-strand | 91 | 1 | 1 |
| β-strand | 95-96 | 2 | 2 |
| β-strand | 113-117 | 5 | 2 |
| α-helix | 122-124 | 3 | |
| β-strand | 128-137 | 10 | 1 |
| α-helix | 141 | 1 | |
| β-strand | 142-143 | 2 | 3 |
| β-strand | 147 | 1 | 4 |
| α-helix | 153-154 | 2 | |
| β-strand | 155-161 | 7 | 3 |
| β-strand | 170 | 1 | 1 |
| β-strand | 173 | 1 | 5 |
| β-strand | 174-178 | 5 | 1 |
| β-strand | 183-185 | 3 | 3 |
| β-strand | 196-198 | 3 | 1 |
| β-strand | 202-205 | 4 | 1 |
| α-helix | 206-207 | 2 | |
| β-strand | 208 | 1 | 5 |
| β-strand | 211 | 1 | 1 |
| β-strand | 219-225 | 7 | 3 |
| β-strand | 231-241 | 11 | 6 |
| β-strand | 248-259 | 12 | 6 |
| α-helix | 262 | 1 | |
| β-strand | 263 | 1 | 4 |
| α-helix | 264 | 1 | |
| α-helix | 270-276 | 7 | |
| β-strand | 288 | 1 | 7 |
| β-strand | 291-293 | 3 | 8 |
| β-strand | 300-306 | 7 | 6 |
| β-strand | 309-310 | 2 | 6 |
| β-strand | 314-317 | 4 | 8 |
| β-strand | 320-323 | 4 | 8 |
| β-strand | 329 | 1 | 7 |
| β-strand | 334-344 | 11 | 6 |
| α-helix | 345-347 | 3 | |
| β-strand | 349-351 | 3 | 9 |
| β-strand | 358-364 | 7 | 9 |
| β-strand | 373-374 | 2 | 6 |
| β-strand | 377-383 | 7 | 6 |
| β-strand | 388-393 | 6 | 9 |
| β-strand | 400-406 | 7 | 6 |
| β-strand | 416-423 | 8 | 6 |
| β-strand | 426-427 | 2 | 6 |
| β-strand | 434-440 | 7 | 9 |
| α-helix | 443-446 | 4 | |
| α-helix | 448-469 | 22 | |
Chain B: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-40 | 17 | |
| α-helix | 42-44 | 3 | |
| α-helix | 45-67 | 23 | |
| α-helix | 74-99 | 26 | |
| α-helix | 109-129 | 21 | |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 216-231 | 16 | |
| α-helix | 234-239 | 6 | |
| β-strand | 246-247 | 2 | 10 |
| β-strand | 253-254 | 2 | 10 |
| α-helix | 265-287 | 23 | |
| α-helix | 288-290 | 3 | |
| α-helix | 296-324 | 29 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-32 | 29 | |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-12 | 10 | |
| α-helix | 16-18 | 3 | |
| α-helix | 25-48 | 24 | |
| α-helix | 53-82 | 30 | |
Chain F: 33 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-30 | 22 | |
| α-helix | 34-37 | 4 | |
| α-helix | 48-60 | 13 | |
| α-helix | 63-67 | 5 | |
| β-strand | 70-71 | 2 | 11 |
| β-strand | 80-81 | 2 | 11 |
| α-helix | 90-103 | 14 | |
| α-helix | 111-137 | 27 | |
| α-helix | 141-151 | 11 | |
| α-helix | 154-157 | 4 | |
| α-helix | 168-188 | 21 | |
| α-helix | 192-207 | 16 | |
| α-helix | 211-227 | 17 | |
| α-helix | 233-250 | 18 | |
| α-helix | 259-262 | 4 | |
| α-helix | 264-287 | 24 | |
| α-helix | 357-361 | 5 | |
| α-helix | 370-379 | 10 | |
| α-helix | 383-401 | 19 | |
| α-helix | 406-429 | 24 | |
| α-helix | 442-469 | 28 | |
| α-helix | 470-474 | 5 | |
| β-strand | 481 | 1 | 12 |
| β-strand | 493 | 1 | 12 |
| α-helix | 496-506 | 11 | |
| β-strand | 512-514 | 3 | 13 |
| α-helix | 520-522 | 3 | |
| α-helix | 523-527 | 5 | |
| β-strand | 530-531 | 2 | 13 |
| α-helix | 541-549 | 9 | |
| α-helix | 554-560 | 7 | |
| β-strand | 568-572 | 5 | 13 |
| α-helix | 587-595 | 9 | |
| α-helix | 604-607 | 4 | |
| α-helix | 628-633 | 6 | |
| α-helix | 637-640 | 4 | |
| β-strand | 646-647 | 2 | 14 |
| β-strand | 654-655 | 2 | 14 |
| α-helix | 661-662 | 2 | |
| β-strand | 666-671 | 6 | 13 |
| β-strand | 677-682 | 6 | 13 |
| α-helix | 683-686 | 4 | |
| α-helix | 692-700 | 9 | |
| α-helix | 715-717 | 3 | |
Chain G: 15 helices, 36 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-29 | 3 | 15 |
| β-strand | 31 | 1 | 16 |
| β-strand | 35 | 1 | 16 |
| α-helix | 37-40 | 4 | |
| α-helix | 41-48 | 8 | |
| β-strand | 55-57 | 3 | 15 |
| α-helix | 65-66 | 2 | |
| β-strand | 69 | 1 | 17 |
| β-strand | 74 | 1 | 17 |
| β-strand | 78-81 | 4 | 15 |
| α-helix | 87-93 | 7 | |
| α-helix | 96-104 | 9 | |
| β-strand | 108-112 | 5 | 15 |
| β-strand | 114 | 1 | 18 |
| β-strand | 117 | 1 | 18 |
| α-helix | 120-129 | 10 | |
| β-strand | 131-132 | 2 | 19 |
| β-strand | 139-141 | 3 | 20 |
| β-strand | 151-154 | 4 | 21 |
| α-helix | 155-157 | 3 | |
| β-strand | 171-174 | 4 | 21 |
| β-strand | 180 | 1 | 22 |
| β-strand | 181-182 | 2 | 19 |
| β-strand | 188-190 | 3 | 15 |
| β-strand | 199-201 | 3 | 20 |
| α-helix | 206-208 | 3 | |
| β-strand | 211 | 1 | 20 |
| α-helix | 212-214 | 3 | |
| β-strand | 216 | 1 | 22 |
| β-strand | 218-222 | 5 | 15 |
| β-strand | 228-232 | 5 | 15 |
| α-helix | 247-257 | 11 | |
| β-strand | 263-273 | 11 | 23 |
| β-strand | 285 | 1 | 24 |
| β-strand | 289-299 | 11 | 23 |
| β-strand | 304-306 | 3 | 23 |
| β-strand | 313-317 | 5 | 25 |
| β-strand | 321-326 | 6 | 25 |
| β-strand | 328-332 | 5 | 23 |
| β-strand | 337-340 | 4 | 23 |
| α-helix | 341-343 | 3 | |
| β-strand | 344-345 | 2 | 23 |
| α-helix | 346-347 | 2 | |
| β-strand | 351-356 | 6 | 25 |
| β-strand | 358-359 | 2 | 26 |
| β-strand | 367-368 | 2 | 26 |
| β-strand | 371-375 | 5 | 25 |
| β-strand | 376 | 1 | 24 |
| α-helix | 380-382 | 3 | |
| α-helix | 384-385 | 2 | |
| α-helix | 394-413 | 20 | |
Chain H: 8 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-33 | 8 | 27 |
| β-strand | 43 | 1 | 28 |
| β-strand | 59-60 | 2 | 27 |
| β-strand | 67-70 | 4 | 27 |
| β-strand | 82-87 | 6 | 28 |
| β-strand | 92-96 | 5 | 28 |
| α-helix | 97-98 | 2 | |
| β-strand | 99-103 | 5 | 27 |
| β-strand | 106-113 | 8 | 27 |
| α-helix | 120-128 | 9 | |
| α-helix | 132 | 1 | |
| β-strand | 133-138 | 6 | 28 |
| β-strand | 151-157 | 7 | 28 |
| β-strand | 180 | 1 | 25 |
| α-helix | 184-189 | 6 | |
| α-helix | 193-212 | 20 | |
| α-helix | 213-217 | 5 | |
| α-helix | 228-251 | 24 | |
| α-helix | 257-281 | 25 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | A | protein | 476 | Saccharomyces cerevisiae S288C | P41543 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 | B | protein | 130 | Saccharomyces cerevisiae S288C | P46964 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 | C | protein | 332 | Saccharomyces cerevisiae S288C | Q03723 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 | D | protein | 36 | Saccharomyces cerevisiae S288C | Q99380 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 | E | protein | 86 | Saccharomyces cerevisiae S288C | Q92316 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 | F | protein | 718 | Saccharomyces cerevisiae S288C | P39007 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 | G | protein | 430 | Saccharomyces cerevisiae S288C | P33767 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 | H | protein | 286 | Saccharomyces cerevisiae S288C | Q02795 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1 | I | protein | 24 | Saccharomyces cerevisiae S288C | |
Sequence of entity 1 (A), FASTA
>7OCI_1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (chains A)
MRQVWFSWIVGLFLCFFNVSSAAQYEPPATWENVDYKRTIDVSNAYISETIEITIKNIAS
EPATEYFTAFESGIFSKVSFFSAYFTNEATFLNSQLLANSTTAPGDDGESEIRYGIIQFP
NAISPQEEVSLVIKSFYNTVGIPYPEHVGMSEEQHLLWETNRLPLSAYDTKKASFTLIGS
SSFEEYHPPNDESLLGKANGNSFEFGPWEDIPRFSSNETLAIVYSHNAPLNQVVNLRRDI
WLSHWASTIQFEEYYELTNKAAKLSKGFSRLELMKQIQTQNMRQTHFVTVLDMLLPEGAT
DHYFTDLVGLVSTSHAERDHFFIRPRFPIFGGWNYNFTVGWTNKLSDFLHVSSGSDEKFV
ASIPILNGPPDTVYDNVELSVFLPEGAEIFDIDSPVPFTNVSIETQKSYFDLNKGHVKLT
FSYRNLISQVANGQVLIKYDYPKSSFFKKPLSIACYIFTALMGVFVLKTLNMNVTN
Sequence of entity 2 (B), FASTA
>7OCI_2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (chains B)
MAKAPKANTPKVTSTSSAVLTDFQETFKTSKRAYFAQIEKYPKLKLIDTFCFFLVLLGVI
QCTFIILIRDNFPFNAFLAGFIICVGQFVLLMSLRLQLCNSFPGISKNRAFAEFIVASLI
LHFVCLHFIN
Sequence of entity 3 (C), FASTA
>7OCI_3 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 (chains C)
MKWCSTYIIIWLAIIFHKFQKSTATASHNIDDILQLKDDTGVITVTADNYPLLSRGVPGY
FNILYITMRGTNSNGMSCQLCHDFEKTYHAVADVIRSQAPQSLNLFFTVDVNEVPQLVKD
LKLQNVPHLVVYPPAESNKQSQFEWKTSPFYQYSLVPENAENTLQFGDFLAKILNISITV
PQAFNVQEFVYYFVACMVVFIFIKKVILPKVTNKWKLFSMILSLGILLPSITGYKFVEMN
AIPFIARDAKNRIMYFSGGSGWQFGIEIFSVSLMYIVMSALSVLLIYVPKISCVSEKMRG
LLSSFLACVLFYFFSYFISCYLIKNPGYPIVF
Sequence of entity 4 (D), FASTA
>7OCI_4 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (chains D)
MISDEQLNSLAITFGIVMMTLIVIYHAVDSTMSPKN
Sequence of entity 5 (E), FASTA
>7OCI_5 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (chains E)
MTYEQLYKEFHSSKSFQPFIHLDTQPKFAICGLIVTLAVLSSALFAVGSKSSYIKKLFFY
TILSVIGSLFAGLTTVFASNSFGVYV
Sequence of entity 6 (F), FASTA
>7OCI_6 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (chains F)
MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVN
NSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAP
LFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFM
FWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYT
TWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMV
SLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFF
FDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVA
LSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVV
LPSQTPDGKLALIDDFREAYYWLRMNSDEDSKVAAWWDYGYQIGGMADRTTLVDNNTWNN
THIAIVGKAMASPEEKSYEILKEHDVDYVLVIFGGLIGFGGDDINKFLWMIRISEGIWPE
EIKERDFYTAEGEYRVDARASETMRNSLLYKMSYKDFPQLFNGGQATDRVRQQMITPLDV
PPLDYFDEVFTSENWMVRIYQLKKDDAQGRTLRDVGELTRSSTKTRRSIKRPELGLRV
Sequence of entity 7 (G), FASTA
>7OCI_7 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains G)
MRTDWNFFFCILLQAIFVVGTQTSRTLVLYDQSTEPLEEYSVYLKDLEQRNYKLEYLDIN
STSTTVDLYDKEQRLFDNIIVFPTKGGKNLARQIPVKQLIKFFENEGNILCMSSPGAVPN
TIRLFLNELGIYPSPKGHVIRDYFSPSSEELVVSSNHLLNKYVYNARKSEDFVFGESSAA
LLENREQIVPILNAPRTSFTESKGKCNSWTSGSQGFLVVGFQNLNNARLVWIGSSDFLKN
KNQDSNQEFAKELLKWTFNEKSVIKSVHAVHSHADGTSYDEEPYKIKDKVIYSVGFSEWN
GEEWLPHIADDIQFELRQVDPYYRLTLSPSGNDSETQYYTTGEFILPDRHGVFTFLTDYR
KIGLSFTTDKDVKAIRHLANDEYPRSWEISNSWVYISAICGVIVAWIFFVVSFVTTSSVG
KKLETFKKTN
Sequence of entity 8 (H), FASTA
>7OCI_8 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (chains H)
MQFFKTLAALVSCISFVLAYVAQDVHVSFPSTAGKSRVMIGKVEPRIGIDETVPTTITVE
DPNEVIQVNFAIESTNKPFQNTLLIGLPNKNLEMAFEPEIKDNGKLSMYKYRIDLAKLDA
ALLQEASRSPEPIKATLILASSTAKPKENLFREILQLNLNFDVDHSDSSLVDKFGIKPEI
HHIFHAEPKRVAKPIAVIFVLIIFITILSLIVTWLNSCAAAFNNIPTGVTAVYFLGFIAT
IVGFEVIFARYYLGTSIFETLFSSLYLGAPGLLTSTKFLRSFGQTI
Sequence of entity 9 (I), FASTA
>7OCI_9 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1 (chains I)
XXXXXXXXXXXXXXXXXXXXXXXX
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 6 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 3 |
| AJP | Digitonin | C56 H92 O29 | 2 |
| MG | Magnesium ion | Mg | 1 |
| V8K | Dolichylphosphate | C55 H91 O4 P | 1 |
Primary citation
Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases. Neuhaus, J.D., Wild, R., Eyring, J. et al. Glycobiology (2021) 31:1604-1615. DOI 10.1093/glycob/cwab084 · PubMed
Other PDB entries of the same protein (UniProt P41543 (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
- 6C26 3.5 Å, The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex
Browse structure collections
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