1RH5: Protein conducting channel

The structure of a protein conducting channel. Determined by X-ray diffraction at 3.2 Å resolution. Released 6 Jan 2004.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Methanocaldococcus jannaschii
Chains: 3
Atoms: 3,852
Mol. weight: 61.93 kDa
Released: 6 Jan 2004

Explore 1RH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RH5 contains 23 α-helices and 7 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: 19 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	15-17	3
α-helix	23-40	18
β-strand	44	1	1
α-helix	45-46	2
α-helix	59-63	5
β-strand	69	1	1
α-helix	76-85	10
α-helix	86-93	8
α-helix	101-128	28
α-helix	137-164	28
α-helix	169-187	19
α-helix	192-199	8
α-helix	207-209	3
α-helix	211-226	16
β-strand	230-234	5	2
β-strand	246-250	5	2
α-helix	257-277	21
β-strand	287	1	3
β-strand	292	1	3
α-helix	298-300	3
α-helix	313-338	26
α-helix	342-348	7
α-helix	363-395	33
α-helix	402-419	18

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	13-23	11
β-strand	25-26	2	2
α-helix	27-29	3
α-helix	30-65	36

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-49	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Preprotein translocase secY subunit	A	protein	436	Methanocaldococcus jannaschii	Q60175 (AlphaFold model)
Preprotein translocase secE subunit	B	protein	74	Methanocaldococcus jannaschii	Q57817 (AlphaFold model)
SecBeta	C	protein	53	Methanocaldococcus jannaschii	P60460 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1RH5_1 Preprotein translocase secY subunit (chains A)
MKKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQ
TITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF
VEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQ
TIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRI
KGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYL
STPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFR
KSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLR
ERTSELHPAIAKLLNK

Sequence of entity 2 (B), FASTA

>1RH5_2 Preprotein translocase secE subunit (chains B)
MKTDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPAT
YIKGILKPPTTPRV

Sequence of entity 3 (C), FASTA

>1RH5_3 SecBeta (chains C)
MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRFL

Primary citation

X-ray structure of a protein-conducting channel. van den Berg, B., Clemons Jr., W.M., Collinson, I. et al. Nature (2004) 427:36-44. DOI 10.1038/nature02218 · PubMed

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

1RHZ 3.5 Å, The structure of a protein conducting channel
2YXQ 3.5 Å, The plug domain of the SecY protein stablizes the closed state of the translocation…
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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