3DL8: Protein translocase subunit secA

Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA. Determined by X-ray diffraction at 7.5 Å resolution. Released 2 Dec 2008.

Method: X-ray diffraction
Resolution: 7.5 Å
Organisms: Bacillus subtilis, Aquifex aeolicus, Aquifex Aeolicus
Chains: 8
Atoms: 10,232
Mol. weight: 311.61 kDa
Released: 2 Dec 2008

Explore 3DL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DL8 contains 96 α-helices and 46 β-strands across 8 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.

Chains A and B: 31 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	9-33	25
α-helix	39-51	13
α-helix	59-76	18
α-helix	86-94	9
β-strand	97-98	2	1
α-helix	107-118	12
β-strand	124-128	5	1
α-helix	131-140	10
α-helix	142-147	6
β-strand	154	1	1
α-helix	164-169	6
β-strand	172-176	5	1
α-helix	177-186	10
β-strand	204-207	4	1
β-strand	221	1	2
α-helix	230-246	17
α-helix	263-271	9
α-helix	284-299	16
β-strand	307	1	3
β-strand	314	1	3
β-strand	316	1	4
β-strand	324	1	4
α-helix	333-341	9
β-strand	352	1	2
α-helix	356-361	6
β-strand	367-370	4	1
α-helix	376-380	5
α-helix	381-385	5
β-strand	401-408	8	5
α-helix	413-428	16
β-strand	432-436	5	5
α-helix	439-452	14
β-strand	457-459	3	5
α-helix	464-473	10
β-strand	480-484	5	5
α-helix	499-501	3
β-strand	506-509	4	5
α-helix	516-524	9
β-strand	534-540	7	5
α-helix	545-548	4
α-helix	551-559	9
β-strand	569	1	5
α-helix	574-619	46
α-helix	624-640	17
α-helix	654-663	10
α-helix	682-701	20
α-helix	705-714	10
α-helix	715-719	5
α-helix	720-741	22
α-helix	750-776	27

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-61	33

Chains E and F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
α-helix	53-70	18

Chains G and H: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	15-33	19
α-helix	77-93	17
α-helix	106-137	32
α-helix	153-157	5
α-helix	158-179	22
α-helix	184-196	13
α-helix	216-232	17
β-strand	245	1	11
β-strand	251	1	11
α-helix	274-290	17
α-helix	308-315	8
α-helix	316-323	8
α-helix	324-327	4
α-helix	332-338	7
β-strand	344	1	12
β-strand	348	1	12
α-helix	353-385	33
α-helix	398-417	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein translocase subunit secA	A, B	protein	779	Bacillus subtilis	P28366 (AlphaFold model)
Preprotein translocase subunit secY	G, H	protein	429	Aquifex aeolicus	O66491 (AlphaFold model)
SecE	C, D	protein	65	Aquifex Aeolicus	D0VWU4 (AlphaFold model)
Protein-export membrane protein secG	E, F	protein	107	Aquifex aeolicus	O66505 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3DL8_1 Protein translocase subunit secA (chains A, B)
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDD
LLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALT
GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNEL
GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF
VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY
FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE
DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV
TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS
MEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDL
INTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAV
DSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAE

Sequence of entity 2 (G, H), FASTA

>3DL8_2 Preprotein translocase subunit secY (chains G, H)
MSEYLKALFELKELRQKFIFTLLMFVIYRLGSHIPIPGINPEALRDFLKAFEGSVFALYD
IFSGGNLGRLTVFALGVMPYISASIMMQLLTVAIPSLQRLAKEEGDYGRYKINEYTKYLT
LFVATVQSLGIAFWIRGQVSPKGIPVVENPGISFILITVLTLVAGTMFLVWIADRITEKG
IGNGASLIIFAGIVANFPNAVIQFYEKVKTGDIGPLTLLLIIALIIAIIVGIVYVQEAER
RIPIQYPGRQVGRQLYAGRKTYLPIKINPAGVIPIIFAQALLLIPSTLLNFVQNPFIKVI
ADMFQPGAIFYNFLYVTFIVFFTYFYTAVLINPVELAENLHKAGAFIPGVRPGQDTVKYL
ERIINRLIFFGALFLSVIALIPILISVWFNIPFYFGGTTALIVVGVALDTFRQIETYLIQ
KKYKSYVRR

Sequence of entity 3 (C, D), FASTA

>3DL8_3 SecE (chains C, D)
MEKLKEFLKGVRDELKRVVWPSRELVVKATISVIIFSLAIGVYLWILDLTFTKIISFILS
LRGSL

Sequence of entity 4 (E, F), FASTA

>3DL8_4 Protein-export membrane protein secG (chains E, F)
MYYALLTLFVIIAVVLIISTLLQKGRGDVGAAFGGGMGQSIFGVGGVETILTKATYWLGA
LFLVLALLLSVIPKEKGSVVEKSVQTEQSEGKGTTQESGKGHHHHHH

Primary citation

Structure of a complex of the ATPase SecA and the protein-translocation channel. Zimmer, J., Nam, Y., Rapoport, T.A. Nature (2008) 455:936-943. DOI 10.1038/nature07335 · PubMed

Other PDB entries of the same protein (UniProt P28366 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TF5 2.18 Å, Crystal structure of SecA in an open conformation from Bacillus Subtilis
3JV2 2.5 Å, Crystal Structure of B. subtilis SecA with bound peptide
1M6N 2.7 Å, Crystal structure of the SecA translocation ATPase from Bacillus subtilis
1TF2 2.9 Å, Crystal structure of SecA:ADP in an open conformation from Bacillus Subtilis
8YA0 2.97 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)
1M74 3.0 Å, Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis
2IBM 3.2 Å, A novel dimer interface and conformational changes revealed by an X-ray structure of B.…
8Y9Y 3.29 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)
3IQY 3.3 Å, Active site mutants of B. subtilis SecA
7XHB 3.33 Å, Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP
7XHA 3.35 Å, Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.
3IQM 3.4 Å, Active site mutants of B. subtilis SecA

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