6Z3T: Canine Sec61 inhibited by mycolactone

Structure of canine Sec61 inhibited by mycolactone. Determined by electron microscopy at 2.69 Å resolution. Released 22 Jul 2020.

Method: Electron microscopy
Resolution: 2.69 Å
Organism: Canis lupus familiaris
Chains: 3
Atoms: 3,608
Mol. weight: 62.49 kDa
Ligands: Q6B
Released: 22 Jul 2020

Explore 6Z3T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z3T contains 21 α-helices and 6 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: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	30-43	14
α-helix	82-96	15
α-helix	110-132	23
α-helix	151-167	17
α-helix	179-193	15
α-helix	213-219	7
α-helix	226-234	9
α-helix	247-259	13
β-strand	262-265	4	1
β-strand	268-269	2	2
β-strand	276	1	2
β-strand	279-282	4	1
α-helix	289-312	24
α-helix	342-344	3
α-helix	346-348	3
α-helix	358-366	9
α-helix	367-371	5
α-helix	372-380	9
α-helix	387-396	10
β-strand	399-400	2	2
α-helix	411-414	4
α-helix	419-433	15
α-helix	446-463	18

Chain B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	9-22	14
β-strand	26	1	1
α-helix	32-64	33

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-47	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein Sec61 subunit alpha isoform 1	A	protein	476	Canis lupus familiaris	P38377 (AlphaFold model)
Protein transport protein Sec61 subunit gamma	B	protein	68	Canis lupus familiaris	P60058 (AlphaFold model)
Protein transport protein Sec61 subunit beta	C	protein	20	Canis lupus familiaris

Sequence of entity 1 (A), FASTA

>6Z3T_1 Protein transport protein Sec61 subunit alpha isoform 1 (chains A)
MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFG
MIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLP
NLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSN
LYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVH
AVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTA
AAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF

Sequence of entity 2 (B), FASTA

>6Z3T_2 Protein transport protein Sec61 subunit gamma (chains B)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG

Sequence of entity 3 (C), FASTA

>6Z3T_3 Protein transport protein Sec61 subunit beta (chains C)
XXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
Q6B	[(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R},7~{R},9~{R})-4,6-dimethyl-7,9…	C44 H70 O9	1

Primary citation

Structure of the Inhibited State of the Sec Translocon. Gerard, S.F., Hall, B.S., Zaki, A.M. et al. Mol Cell (2020) 79:406-415.e7. DOI 10.1016/j.molcel.2020.06.013 · PubMed

Other PDB entries of the same protein (UniProt P38377 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8RJC 2.9 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
7TM3 3.25 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in…
8OJ8 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)
8BTK 3.5 Å, Structure of the TRAP complex with the Sec translocon and a translating ribosome
3JC2 3.6 Å, The structure of the mammalian Sec61 channel opened by a signal sequence
7TUT 3.88 Å, Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in…
6R7Q 3.9 Å, Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
6FTI 4.2 Å, Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the…
6FTJ 4.7 Å, Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the…
2WWB 6.48 Å, cryo-EM structure of the mammalian SEC61 complex bound to the actively translating wheat…

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