3DKN: Preprotein translocase subunit secY

Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum. Determined by electron microscopy at 8.7 Å resolution. Released 19 Aug 2008.

Method
Electron microscopy
Resolution
8.7 Å
Organism
Canis lupus familiaris
Chains
6
Atoms
5,554
Mol. weight
80.07 kDa
Released
19 Aug 2008

Explore 3DKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DKN contains 22 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

ElementResiduesLengthSheet
α-helix5-106
β-strand1411
α-helix23-4220
β-strand4412
α-helix451
α-helix60-634
β-strand6912
α-helix76-8813
α-helix101-12828
α-helix137-16428
α-helix169-18719
α-helix192-20211
α-helix207-22822
α-helix253-2553
α-helix256-27520
α-helix295-2995
α-helix313-33220
β-strand33513
β-strand33813
α-helix343-3486
α-helix364-3707
α-helix377-39317
α-helix399-42224
Chain B: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix3-2119
α-helix27-293
α-helix30-6435
Chain C: 1 helix, 1 β-strand
ElementResiduesLengthSheet
β-strand2811
α-helix31-4717

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA (5'-r(p*cp*gp*up*gp*cp*cp*ap*ap*gp*cp*up*gp*cp*gp*ap*up*ap*ap*gp*c)-3')DRNA20Canis lupus familiaris
RNA (5'-r(p*ap*gp*cp*cp*gp*cp*ap*cp*gp*gp*ap*gp*gp*cp*gp*ap*a)-3')ERNA17Canis lupus familiaris
RNA (32-mer)FRNA32Canis lupus familiaris
Preprotein translocase subunit secYAprotein430Canis lupus familiarisQ60175 (AlphaFold model)
Preprotein translocase subunit secEBprotein65Canis lupus familiarisQ57817 (AlphaFold model)
Preprotein translocase subunit secGCprotein32Canis lupus familiarisP60460 (AlphaFold model)
Sequence of entity 1 (D), FASTA
>3DKN_1 RNA (5'-R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3') (chains D)
CGUGCCAAGCUGCGAUAAGC
Sequence of entity 2 (E), FASTA
>3DKN_2 RNA (5'-R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3') (chains E)
AGCCGCACGGAGGCGAA
Sequence of entity 3 (F), FASTA
>3DKN_3 RNA (32-MER) (chains F)
GGGUUCCUCAGCACUGCUGAUCAGCUGAGGGU
Sequence of entity 4 (A), FASTA
>3DKN_4 Preprotein translocase subunit secY (chains A)
KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQT
ITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFV
EAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQT
IFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIK
GAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLS
TPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRK
SAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKV
SELHPAIAKL
Sequence of entity 5 (B), FASTA
>3DKN_5 Preprotein translocase subunit secE (chains B)
TDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYI
KGILK
Sequence of entity 6 (C), FASTA
>3DKN_6 Preprotein translocase subunit secG (chains C)
ETFSKIRVKPEHVIGVTVAFVIIEAILTYGRF

Primary citation

Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Menetret, J.F., Hegde, R.S., Aguiar, M. et al. Structure (2008) 16:1126-1137. DOI 10.1016/j.str.2008.05.003 · PubMed

Other PDB entries of the same protein (UniProt Q60175 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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