2YXQ: Preprotein translocase subunit secY

The plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal. Determined by X-ray diffraction at 3.5 Å resolution. Released 14 Aug 2007.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Methanocaldococcus jannaschii
Chains: 3
Atoms: 4,052
Mol. weight: 61.36 kDa
Released: 14 Aug 2007

Explore 2YXQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YXQ contains 21 α-helices and 11 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	14	1	1
α-helix	23-42	20
β-strand	44	1	2
α-helix	45	1
α-helix	54-57	4
β-strand	69	1	2
α-helix	76-88	13
α-helix	101-128	28
α-helix	137-164	28
α-helix	169-187	19
α-helix	192-202	11
α-helix	207-228	22
β-strand	231-232	2	3
β-strand	235	1	4
β-strand	236	1	5
β-strand	243	1	5
β-strand	248-249	2	3
α-helix	253-255	3
α-helix	256-275	20
α-helix	295-299	5
α-helix	313-335	23
α-helix	342-351	10
β-strand	356	1	4
α-helix	363-395	33
α-helix	401-424	24

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-21	19
β-strand	25	1	3
α-helix	27-29	3
α-helix	30-64	35

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	28	1	1
α-helix	31-47	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Preprotein translocase subunit secY	A	protein	431	Methanocaldococcus jannaschii	Q60175 (AlphaFold model)
Preprotein translocase subunit secE	B	protein	74	Methanocaldococcus jannaschii	Q57817 (AlphaFold model)
Preprotein translocase secG subunit	C	protein	53	Methanocaldococcus jannaschii	P60460 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YXQ_1 Preprotein translocase subunit secY (chains A)
MKKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWG
RIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVL
FVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVG
ALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVG
KYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYG
LSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKA
IEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKVSE
LHPAIAKLLNK

Sequence of entity 2 (B), FASTA

>2YXQ_2 Preprotein translocase subunit secE (chains B)
MKTDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPAT
YIKGILKPPTTPRV

Sequence of entity 3 (C), FASTA

>2YXQ_3 Preprotein translocase secG subunit (chains C)
MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRFL

Primary citation

The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal. Li, W., Schulman, S., Boyd, D. et al. Mol Cell (2007) 26:511-521. DOI 10.1016/j.molcel.2007.05.002 · PubMed

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

1RH5 3.2 Å, The structure of a protein conducting channel
1RHZ 3.5 Å, The structure of a protein conducting channel
2YXR 3.6 Å, The plug domain of the SecY protein stablizes the closed state of the translocation…
3DKN 8.7 Å, Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum
4V4N 9.0 Å, Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex
3BO0 9.6 Å, Ribosome-SecY complex
3BO1 9.6 Å, Ribosome-SecY complex

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