8DNY: Human Sec61 complex inhibited by decatransin

Cryo-EM structure of the human Sec61 complex inhibited by decatransin. Determined by electron microscopy at 2.85 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 2.85 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,331
Mol. weight: 71.14 kDa
Released: 24 May 2023

Explore 8DNY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DNY contains 26 α-helices and 12 β-strands across 3 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: 23 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
β-strand	18-19	2	1
α-helix	20-22	3
α-helix	25-27	3
α-helix	28-47	20
β-strand	49	1	2
α-helix	50	1
β-strand	75	1	2
α-helix	82-96	15
α-helix	106-133	28
α-helix	140-168	29
α-helix	169-173	5
α-helix	178-196	19
β-strand	200	1	3
β-strand	209	1	3
α-helix	212-222	11
α-helix	227-235	9
α-helix	242-259	18
β-strand	262-269	8	4
β-strand	277-282	6	4
α-helix	289-311	23
α-helix	316-321	6
β-strand	323-324	2	5
β-strand	337-339	3	5
α-helix	340-344	5
α-helix	347-348	2
α-helix	351-356	6
α-helix	358-382	25
α-helix	387-395	9
β-strand	399-401	3	4
α-helix	406-408	3
α-helix	409-438	30
α-helix	443-467	25

Chain B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	26	1	4
α-helix	30-65	36

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	67-68	2	1
α-helix	70-95	26

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 gamma	B	protein	68	Homo sapiens	P60059 (AlphaFold model)
Protein transport protein Sec61 subunit beta	C	protein	96	Homo sapiens	P60468 (AlphaFold model)
Decatransin peptide inhibitor	D	protein	10	synthetic construct

Sequence of entity 1 (A), FASTA

>8DNY_1 Protein transport protein Sec61 subunit alpha isoform 1 (chains A)
MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFG
MIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLP
NLMNLIATIFVFAVVIYFQGFRYELPIRSTKVRGQIGIYPIKLFYTSNIPIILQSALVSN
LYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCYYLSPPESFGSVLEDPVH
AVVYIVFMLGSCAFFSKTWIEVSGSSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPTA
AAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF

Sequence of entity 2 (B), FASTA

>8DNY_2 Protein transport protein Sec61 subunit gamma (chains B)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG

Sequence of entity 3 (C), FASTA

>8DNY_3 Protein transport protein Sec61 subunit beta (chains C)
MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYT
EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS

Sequence of entity 4 (D), FASTA

>8DNY_4 Decatransin peptide inhibitor (chains D)
AXIXXXLTXL

Primary citation

A common mechanism of Sec61 translocon inhibition by small molecules. Itskanov, S., Wang, L., Junne, T. et al. Nat Chem Biol (2023) 19:1063-1071. DOI 10.1038/s41589-023-01337-y · 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
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)
8DNW 3.4 Å, Cryo-EM structure of the human Sec61 complex in a partially-open apo state (Class 2)

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