9YGY: Translocon-associated protein subunit alpha
Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon. Determined by electron microscopy at 4.1 Å resolution. Released 19 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organism
- Homo sapiens
- Chains
- 20
- Atoms
- 37,161
- Mol. weight
- 645.91 kDa
- Ligands
- ELU
- Released
- 19 Nov 2025
Explore 9YGY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9YGY contains 203 α-helices and 186 β-strands across 20 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 5: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 78-80 | 3 | |
| β-strand | 83-84 | 2 | 1 |
| β-strand | 87-89 | 3 | 2 |
| β-strand | 101-105 | 5 | 2 |
| β-strand | 108-109 | 2 | 1 |
| β-strand | 115-125 | 11 | 3 |
| β-strand | 133-146 | 14 | 3 |
| β-strand | 151-152 | 2 | 4 |
| β-strand | 154-158 | 5 | 2 |
| α-helix | 162-164 | 3 | |
| β-strand | 167-179 | 13 | 3 |
| β-strand | 184-196 | 13 | 3 |
| α-helix | 197-198 | 2 | |
| α-helix | 258-264 | 7 | |
Chain 6: 6 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-29 | 7 | 5 |
| β-strand | 31 | 1 | 6 |
| β-strand | 34-35 | 2 | 7 |
| β-strand | 40-48 | 9 | 5 |
| β-strand | 54-60 | 7 | 4 |
| β-strand | 69 | 1 | 8 |
| β-strand | 73 | 1 | 5 |
| β-strand | 78-83 | 6 | 4 |
| β-strand | 88-95 | 8 | 5 |
| β-strand | 97 | 1 | 8 |
| β-strand | 102 | 1 | 9 |
| β-strand | 105 | 1 | 10 |
| α-helix | 107-108 | 2 | |
| β-strand | 109-113 | 5 | 4 |
| α-helix | 118-119 | 2 | |
| β-strand | 120-124 | 5 | 4 |
| β-strand | 129 | 1 | 10 |
| β-strand | 132 | 1 | 9 |
| β-strand | 133-134 | 2 | 7 |
| α-helix | 136-143 | 8 | |
| α-helix | 149-157 | 9 | |
| α-helix | 158-162 | 5 | |
| α-helix | 163-175 | 13 | |
Chain 7: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-20 | 13 | |
| α-helix | 24-25 | 2 | |
| α-helix | 26-46 | 21 | |
| α-helix | 47-51 | 5 | |
| α-helix | 55-107 | 53 | |
| α-helix | 114-151 | 38 | |
| α-helix | 152-156 | 5 | |
| α-helix | 162-184 | 23 | |
Chain 8: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30 | 1 | 11 |
| β-strand | 34-37 | 4 | 4 |
| β-strand | 40 | 1 | 12 |
| β-strand | 44 | 1 | 6 |
| β-strand | 47-54 | 8 | 4 |
| β-strand | 56 | 1 | 11 |
| β-strand | 67-70 | 4 | 13 |
| β-strand | 73-76 | 4 | 13 |
| α-helix | 77 | 1 | |
| β-strand | 78-80 | 3 | 4 |
| β-strand | 85-92 | 8 | 4 |
| β-strand | 100-107 | 8 | 13 |
| α-helix | 109-121 | 13 | |
| α-helix | 125-127 | 3 | |
| β-strand | 132-138 | 7 | 13 |
| β-strand | 142 | 1 | 12 |
| α-helix | 150-172 | 23 | |
Chain A: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-17 | 6 | 14 |
| β-strand | 32-41 | 10 | 14 |
| β-strand | 46-49 | 4 | 14 |
| α-helix | 55 | 1 | |
| β-strand | 56-59 | 4 | 14 |
| α-helix | 67-73 | 7 | |
| β-strand | 81-86 | 6 | 14 |
| α-helix | 88-90 | 3 | |
| α-helix | 93-95 | 3 | |
| β-strand | 97 | 1 | 15 |
| β-strand | 101 | 1 | 15 |
| β-strand | 107-117 | 11 | 14 |
| α-helix | 118-120 | 3 | |
| α-helix | 121-153 | 33 | |
| α-helix | 160-172 | 13 | |
Chain B: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-55 | 26 | |
| α-helix | 59-87 | 29 | |
| α-helix | 95-96 | 2 | |
| α-helix | 99-121 | 23 | |
| α-helix | 123-130 | 8 | |
| α-helix | 134-150 | 17 | |
| α-helix | 152-154 | 3 | |
| α-helix | 159-169 | 11 | |
| α-helix | 173-175 | 3 | |
| α-helix | 195-217 | 23 | |
Chain D: 24 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-15 | 14 | |
| β-strand | 18-19 | 2 | 16 |
| α-helix | 20-22 | 3 | |
| α-helix | 25-27 | 3 | |
| α-helix | 28-47 | 20 | |
| α-helix | 48 | 1 | |
| β-strand | 49 | 1 | 17 |
| α-helix | 50 | 1 | |
| α-helix | 63-68 | 6 | |
| β-strand | 75 | 1 | 17 |
| α-helix | 82-97 | 16 | |
| α-helix | 106-134 | 29 | |
| α-helix | 140-143 | 4 | |
| α-helix | 145-171 | 27 | |
| α-helix | 178-196 | 19 | |
| β-strand | 200-202 | 3 | 18 |
| β-strand | 207-209 | 3 | 18 |
| α-helix | 212-222 | 11 | |
| α-helix | 226-235 | 10 | |
| α-helix | 242-259 | 18 | |
| β-strand | 262-269 | 8 | 19 |
| β-strand | 276-282 | 7 | 19 |
| α-helix | 289-311 | 23 | |
| α-helix | 316-321 | 6 | |
| β-strand | 323-324 | 2 | 20 |
| β-strand | 337-339 | 3 | 20 |
| α-helix | 341-345 | 5 | |
| α-helix | 347-348 | 2 | |
| α-helix | 351-356 | 6 | |
| α-helix | 358-383 | 26 | |
| α-helix | 387-397 | 11 | |
| β-strand | 399-400 | 2 | 19 |
| α-helix | 406-438 | 33 | |
| α-helix | 444-465 | 22 | |
Chain E: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 67-68 | 2 | 16 |
| α-helix | 70-95 | 26 | |
12 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 |
|---|
| Translocon-associated protein subunit alpha | 5 | protein | 286 | Homo sapiens | P43307 (AlphaFold model) |
| Translocon-associated protein subunit beta | 6 | protein | 183 | Homo sapiens | P43308 (AlphaFold model) |
| Translocon-associated protein subunit gamma | 7 | protein | 185 | Homo sapiens | Q9UNL2 (AlphaFold model) |
| Translocon-associated protein subunit delta | 8 | protein | 173 | Homo sapiens | P51571 (AlphaFold model) |
| Peptidyl-prolyl cis-trans isomerase FKBP11 | A | protein | 201 | Homo sapiens | Q9NYL4 |
| Coiled-coil domain-containing protein 134 | B | protein | 229 | Homo sapiens | Q9H6E4 |
| Protein transport protein Sec61 subunit alpha isoform 1 | D | protein | 476 | Homo sapiens | P61619 |
| Protein transport protein Sec61 subunit beta | E | protein | 96 | Homo sapiens | P60468 |
| Protein transport protein Sec61 subunit gamma | F | protein | 68 | Homo sapiens | P60059 |
| Stress-associated endoplasmic reticulum protein 1 | G | protein | 66 | Homo sapiens | Q9Y6X1 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A | I | protein | 705 | Homo sapiens | P46977 |
| Oligosaccharyltransferase complex subunit OSTC | J | protein | 149 | Homo sapiens | Q9NRP0 |
8 more molecules are not listed.
Sequence of entity 1 (5), FASTA
>9YGY_1 Translocon-associated protein subunit alpha (chains 5)
MRLLPRLLLLLLLVFPATVLFRGGPRGLLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDE
PTDLVEDKEEEDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESL
DASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDL
NGNVFQDAVFNQTVTVIEREDGLDGETIFMYMFLAGLGLLVIVGLHQLLESRKRKRPIQK
VEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE
Sequence of entity 2 (6), FASTA
>9YGY_2 Translocon-associated protein subunit beta (chains 6)
MRLLSFVVLALFAVTQAEEGARLLASKSLLNRYAVEGRDLTLQYNIYNVGSSAALDVELS
DDSFPPEDFGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATITYLAQEDGPV
VIGSTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKT
KKN
Sequence of entity 3 (7), FASTA
>9YGY_3 Translocon-associated protein subunit gamma (chains 7)
MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAV
LYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDER
ILWKKNEVADYEATTFSIFYNNTLFLVVVIVASFFILKNFNPTVNYILSISASSGLIALL
STGSK
Sequence of entity 4 (8), FASTA
>9YGY_4 Translocon-associated protein subunit delta (chains 8)
MAAMASLGALALLLLSSLSRCSAEACLEPQITPSYYTTSDAVISTETVFIVEISLTCKNR
VQNMALYADVGGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQR
NNEDISIIPPLFTVSVDHRGTWNGPWVSTEVLAAAIGLVIYYLAFSAKSHIQA
Sequence of entity 5 (A), FASTA
>9YGY_5 Peptidyl-prolyl cis-trans isomerase FKBP11 (chains A)
MTLRPSLLPLHLLLLLLLSAAVCRAEAGLETESPVRTLQVETLVEPPEPCAEPAAFGDTL
HIHYTGSLVDGRIIDTSLTRDPLVIELGQKQVIPGLEQSLLDMCVGEKRRAIIPSHLAYG
KRGFPPSVPADAVVQYDVELIALIRANYWLKLVKGILPLVGMAMVPALLGLIGYHLYRKA
NRPKVSKKKLKEEKRNKSKKK
Sequence of entity 6 (B), FASTA
>9YGY_6 Coiled-coil domain-containing protein 134 (chains B)
MDLLQFLAFLFVLLLSGMGATGTLRTSLDPSLEIYKKMFEVKRREQLLALKNLAQLNDIH
QQYKILDVMLKGLFKVLEDSRTVLTAADVLPDGPFPQDEKLKDAFSHVVENTAFFGDVVL
RFPRIVHYYFDHNSNWNLLIRWGISFCNQTGVFNQGPHSPILSLMAQELGISEKDSNFQN
PFKIDRTEFIPSTDPFQKALREEEKRRKKEEKRKEIRKGPRISRSQSEL
Sequence of entity 7 (D), FASTA
>9YGY_7 Protein transport protein Sec61 subunit alpha isoform 1 (chains D)
MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFG
MIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLP
NLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSN
LYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCYYLSPPESFGSVLEDPVH
AVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTA
AAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF
Sequence of entity 8 (E), FASTA
>9YGY_8 Protein transport protein Sec61 subunit beta (chains E)
MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYT
EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS
Sequence of entity 9 (F), FASTA
>9YGY_9 Protein transport protein Sec61 subunit gamma (chains F)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG
Sequence of entity 10 (G), FASTA
>9YGY_10 Stress-associated endoplasmic reticulum protein 1 (chains G)
MVAKQRIRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQ
SIRMGM
Sequence of entity 11 (I), FASTA
>9YGY_11 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A (chains I)
MTKFGFLRLSYEKQDTLLKLLILSMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFL
AEEGFYKFHNWFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLA
PLFSSFTTIVTYHLTKELKDAGAGLLAAAMIAVVPGYISRSVAGSYDNEGIAIFCMLLTY
YMWIKAVKTGSICWAAKCALAYFYMVSSWGGYVFLINLIPLHVLVLMLTGRFSHRIYVAY
CTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQIHAFVDYLRSKLNPQQFEVLFR
SVISLVGFVLLTVGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVSEHQPTTWSSY
YFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVMVRLMLVLAPVMCILSGI
GVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTS
EAYSSPSIVLSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTI
LVDNNTWNNTHISRVGQAMASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMV
RIGGSTDTGKHIKENDYYTPTGEFRVDREGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGF
DRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLDNRGLSRT
Sequence of entity 12 (J), FASTA
>9YGY_12 Oligosaccharyltransferase complex subunit OSTC (chains J)
METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVG
SMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLL
LFIGFVCVLLSFFMARVFMRMKLPGYLMG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ELU | phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl]… | C20 H38 O7 P2 | 1 |
Primary citation
Structural basis of regulated N-glycosylation at the secretory translocon. Yamsek, M., Ma, M., Jha, R. et al. Nature (2026) 649:777-784. DOI 10.1038/s41586-025-09756-8 · PubMed
Other PDB entries of the same protein (UniProt P43307 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9N9J 3.2 Å, Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound…
- 8B6L 7.6 Å, Subtomogram average of the human Sec61-TRAP-OSTA-translocon
Browse structure collections
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