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
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
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
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
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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