8B6L: PDB entry 8B6L
Subtomogram average of the human Sec61-TRAP-OSTA-translocon. Determined by electron microscopy at 7.6 Å resolution. Released 7 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 7.6 Å
- Organism
- Homo sapiens
- Chains
- 16
- Atoms
- 29,611
- Mol. weight
- 476.57 kDa
- Released
- 7 Dec 2022
Explore 8B6L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8B6L contains 180 α-helices and 151 β-strands across 16 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: 28 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 10-12 | 3 | |
| α-helix | 20-22 | 3 | |
| α-helix | 28-47 | 20 | |
| α-helix | 63-68 | 6 | |
| α-helix | 82-94 | 13 | |
| α-helix | 99-102 | 4 | |
| α-helix | 106-108 | 3 | |
| α-helix | 111-134 | 24 | |
| α-helix | 146-168 | 23 | |
| α-helix | 169-173 | 5 | |
| α-helix | 178-196 | 19 | |
| β-strand | 200-201 | 2 | 1 |
| β-strand | 208-209 | 2 | 1 |
| α-helix | 215-222 | 8 | |
| α-helix | 226-235 | 10 | |
| α-helix | 242-259 | 18 | |
| β-strand | 263-266 | 4 | 2 |
| β-strand | 268 | 1 | 3 |
| β-strand | 272-275 | 4 | 2 |
| α-helix | 279-282 | 4 | |
| α-helix | 284-302 | 19 | |
| β-strand | 307-309 | 3 | 4 |
| β-strand | 313-316 | 4 | 4 |
| α-helix | 317-322 | 6 | |
| α-helix | 328-333 | 6 | |
| α-helix | 336-350 | 15 | |
| α-helix | 352-355 | 4 | |
| α-helix | 356-360 | 5 | |
| α-helix | 364-374 | 11 | |
| β-strand | 377 | 1 | 3 |
| α-helix | 386-391 | 6 | |
| α-helix | 393-396 | 4 | |
| α-helix | 399-403 | 5 | |
| α-helix | 404-415 | 12 | |
| α-helix | 420-447 | 28 | |
Chain B: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-73 | 2 | |
| α-helix | 74-78 | 5 | |
| α-helix | 79-82 | 4 | |
| α-helix | 84-89 | 6 | |
Chain C: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-25 | 24 | |
| α-helix | 30-54 | 25 | |
| α-helix | 55-57 | 3 | |
| α-helix | 58-61 | 4 | |
| α-helix | 62-64 | 3 | |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-10 | 8 | |
| α-helix | 11-16 | 6 | |
| α-helix | 17-21 | 5 | |
Chain E: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 83-89 | 7 | 5 |
| β-strand | 101-109 | 9 | 5 |
| β-strand | 115-126 | 12 | 6 |
| β-strand | 129-136 | 8 | 6 |
| α-helix | 137-139 | 3 | |
| β-strand | 140-146 | 7 | 6 |
| β-strand | 150-158 | 9 | 5 |
| α-helix | 162-164 | 3 | |
| β-strand | 169-179 | 11 | 6 |
| β-strand | 184-194 | 11 | 6 |
| α-helix | 206-208 | 3 | |
| α-helix | 209-213 | 5 | |
| α-helix | 215-230 | 16 | |
Chain F: 6 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-29 | 7 | 7 |
| β-strand | 34-35 | 2 | 8 |
| β-strand | 40-48 | 9 | 7 |
| β-strand | 54-60 | 7 | 5 |
| β-strand | 69-73 | 5 | 7 |
| β-strand | 77-83 | 7 | 5 |
| β-strand | 88-97 | 10 | 7 |
| β-strand | 101-105 | 5 | 8 |
| α-helix | 106-108 | 3 | |
| β-strand | 109-113 | 5 | 5 |
| α-helix | 118-119 | 2 | |
| β-strand | 120-124 | 5 | 5 |
| β-strand | 129-134 | 6 | 8 |
| α-helix | 136-143 | 8 | |
| α-helix | 148-156 | 9 | |
| α-helix | 158-161 | 4 | |
| α-helix | 162-175 | 14 | |
Chain G: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-36 | 8 | |
| α-helix | 38-41 | 4 | |
| α-helix | 44-49 | 6 | |
| α-helix | 59-102 | 44 | |
| α-helix | 115-120 | 6 | |
| α-helix | 121-125 | 5 | |
| α-helix | 126-151 | 26 | |
| α-helix | 152-156 | 5 | |
| α-helix | 157-159 | 3 | |
| α-helix | 162-181 | 20 | |
Chain H: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-37 | 8 | 9 |
| β-strand | 46-56 | 11 | 9 |
| β-strand | 67-70 | 4 | 10 |
| β-strand | 73-76 | 4 | 10 |
| α-helix | 77 | 1 | |
| β-strand | 78-79 | 2 | 9 |
| α-helix | 80 | 1 | |
| β-strand | 85-93 | 9 | 9 |
| β-strand | 100-107 | 8 | 10 |
| α-helix | 109-121 | 13 | |
| α-helix | 125-127 | 3 | |
| β-strand | 132-138 | 7 | 10 |
| α-helix | 150-172 | 23 | |
8 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 |
|---|
| Protein transport protein Sec61 subunit alpha isoform 1 | A | protein | 476 | Homo sapiens | P61619 (AlphaFold model) |
| Protein transport protein Sec61 subunit beta | B | protein | 96 | Homo sapiens | P60468 (AlphaFold model) |
| Protein transport protein Sec61 subunit gamma | C | protein | 68 | Homo sapiens | P60059 (AlphaFold model) |
| Signal peptide mix | D | protein | 22 | Homo sapiens | |
| Translocon-associated protein subunit alpha | E | protein | 286 | Homo sapiens | P43307 (AlphaFold model) |
| Translocon-associated protein subunit beta | F | protein | 183 | Homo sapiens | P43308 |
| Translocon-associated protein subunit gamma | G | protein | 185 | Homo sapiens | Q9UNL2 |
| Translocon-associated protein subunit delta | H | protein | 173 | Homo sapiens | P51571 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A | I | protein | 705 | Homo sapiens | P46977 |
| Oligosaccharyltransferase complex subunit OSTC | J | protein | 149 | Homo sapiens | Q9NRP0 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 | K | protein | 37 | Homo sapiens | P0C6T2 |
| Transmembrane protein 258 | L | protein | 79 | Homo sapiens | P61165 |
4 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8B6L_1 Protein transport protein Sec61 subunit alpha isoform 1 (chains A)
MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFG
MIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLP
NLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSN
LYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCYYLSPPESFGSVLEDPVH
AVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTA
AAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF
Sequence of entity 2 (B), FASTA
>8B6L_2 Protein transport protein Sec61 subunit beta (chains B)
MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYT
EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS
Sequence of entity 3 (C), FASTA
>8B6L_3 Protein transport protein Sec61 subunit gamma (chains C)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG
Sequence of entity 4 (D), FASTA
>8B6L_4 Signal peptide mix (chains D)
XXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 5 (E), FASTA
>8B6L_5 Translocon-associated protein subunit alpha (chains E)
MRLLPRLLLLLLLVFPATVLFRGGPRGLLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDE
PTDLVEDKEEEDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESL
DASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDL
NGNVFQDAVFNQTVTVIEREDGLDGETIFMYMFLAGLGLLVIVGLHQLLESRKRKRPIQK
VEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE
Sequence of entity 6 (F), FASTA
>8B6L_6 Translocon-associated protein subunit beta (chains F)
MRLLSFVVLALFAVTQAEEGARLLASKSLLNRYAVEGRDLTLQYNIYNVGSSAALDVELS
DDSFPPEDFGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATITYLAQEDGPV
VIGSTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKT
KKN
Sequence of entity 7 (G), FASTA
>8B6L_7 Translocon-associated protein subunit gamma (chains G)
MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAV
LYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDER
ILWKKNEVADYEATTFSIFYNNTLFLVVVIVASFFILKNFNPTVNYILSISASSGLIALL
STGSK
Sequence of entity 8 (H), FASTA
>8B6L_8 Translocon-associated protein subunit delta (chains H)
MAAMASLGALALLLLSSLSRCSAEACLEPQITPSYYTTSDAVISTETVFIVEISLTCKNR
VQNMALYADVGGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQR
NNEDISIIPPLFTVSVDHRGTWNGPWVSTEVLAAAIGLVIYYLAFSAKSHIQA
Sequence of entity 9 (I), FASTA
>8B6L_9 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A (chains I)
MTKFGFLRLSYEKQDTLLKLLILSMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFL
AEEGFYKFHNWFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLA
PLFSSFTTIVTYHLTKELKDAGAGLLAAAMIAVVPGYISRSVAGSYDNEGIAIFCMLLTY
YMWIKAVKTGSICWAAKCALAYFYMVSSWGGYVFLINLIPLHVLVLMLTGRFSHRIYVAY
CTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQIHAFVDYLRSKLNPQQFEVLFR
SVISLVGFVLLTVGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVSEHQPTTWSSY
YFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVMVRLMLVLAPVMCILSGI
GVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTS
EAYSSPSIVLSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTI
LVDNNTWNNTHISRVGQAMASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMV
RIGGSTDTGKHIKENDYYTPTGEFRVDREGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGF
DRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLDNRGLSRT
Sequence of entity 10 (J), FASTA
>8B6L_10 Oligosaccharyltransferase complex subunit OSTC (chains J)
METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVG
SMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLL
LFIGFVCVLLSFFMARVFMRMKLPGYLMG
Sequence of entity 11 (K), FASTA
>8B6L_11 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (chains K)
MITDVQLAIFANMLGVSLFLLVVLYHYVAVNNPKKQE
Sequence of entity 12 (L), FASTA
>8B6L_12 Transmembrane protein 258 (chains L)
MELEAMSRYTSPVNPAVFPHLTVVLLAIGMFFTAWFFVYEVTSTKYTRDIYKELLISLVA
SLFMGFGVLFLLLWVGIYV
Primary citation
Visualization of translation and protein biogenesis at the ER membrane. Gemmer, M., Chaillet, M.L., van Loenhout, J. et al. Nature (2023) 614:160-167. DOI 10.1038/s41586-022-05638-5 · PubMed
Other PDB entries of the same protein (UniProt P61619 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8DNZ 2.57 Å, Cryo-EM structure of the human Sec61 complex inhibited by apratoxin F
- 8DNY 2.85 Å, Cryo-EM structure of the human Sec61 complex inhibited by decatransin
- 8DO0 2.86 Å, Cryo-EM structure of the human Sec61 complex inhibited by mycolactone
- 8DO2 2.95 Å, Cryo-EM structure of the human Sec61 complex inhibited by cyclotriazadisulfonamide (CADA)
- 8DNX 2.98 Å, Cryo-EM structure of the human Sec61 complex inhibited by cotransin
- 8DO1 3.01 Å, Cryo-EM structure of the human Sec61 complex inhibited by ipomoeassin F
- 8DNV 3.03 Å, Cryo-EM structure of the human Sec61 complex in a partially-open apo state (Class 1)
- 9D6L 3.1 Å, Human Sec61 complex inhibited by KZR-261
- 9YWS 3.1 Å, Human Sec61 complex bound to coibamide A
- 9N9J 3.2 Å, Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound…
- 8DO3 3.22 Å, Cryo-EM structure of the human Sec61 complex inhibited by eeyarestatin I
- 8OJ0 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)
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