5EUL: PDB entry 5EUL

Structure of the SecA-SecY complex with a translocating polypeptide substrate. Determined by X-ray diffraction at 3.7 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 3.7 Å
Organisms: Bacillus subtilis (strain 168), synthetic construct, Bacillus subtilis
Chains: 4
Atoms: 10,511
Mol. weight: 201.17 kDa
Ligands: BEF, TBR, ADP, MG
Released: 9 Mar 2016

Explore 5EUL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EUL contains 57 α-helices and 45 β-strands across 4 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: 38 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	16-28	13
α-helix	31-34	4
α-helix	37-53	17
α-helix	58-76	19
α-helix	79-82	4
α-helix	83-93	11
β-strand	97-99	3	1
α-helix	106-118	13
β-strand	124-128	5	1
α-helix	131-147	17
β-strand	152-154	3	1
α-helix	161-169	9
β-strand	172-176	5	1
α-helix	177-187	11
α-helix	193-195	3
β-strand	203-207	5	1
α-helix	209-210	2
α-helix	211-215	5
β-strand	220-226	7	2
α-helix	234-240	7
β-strand	251	1	3
β-strand	258	1	3
α-helix	263-272	10
α-helix	281-283	3
α-helix	286-298	13
β-strand	303	1	4
β-strand	306-309	4	4
β-strand	312-316	5	4
α-helix	317	1
β-strand	323-324	2	4
α-helix	333-340	8
α-helix	347-348	2
β-strand	349-356	8	2
α-helix	357-361	5
β-strand	367-371	5	1
α-helix	374-377	4
α-helix	378-383	6
β-strand	389-391	3	1
β-strand	401-402	2	5
α-helix	403-405	3
β-strand	406-408	3	6
α-helix	412-427	16
β-strand	432-435	4	5
α-helix	439-450	12
β-strand	457-459	3	5
α-helix	467-474	8
β-strand	480-483	4	5
α-helix	485-487	3
α-helix	500-502	3
β-strand	506-509	4	5
α-helix	516-524	9
β-strand	534-537	4	5
β-strand	538-540	3	6
α-helix	544-547	4
α-helix	554-560	7
β-strand	569	1	6
α-helix	572-618	47
α-helix	626-641	16
α-helix	685-698	14
α-helix	707-736	30
α-helix	754-769	16
β-strand	770	1	7
α-helix	797-823	27

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	24-54	31

Chain V: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	11-12	2	12
β-strand	18-24	7	11
β-strand	33-37	5	13
β-strand	47-52	6	13
β-strand	57-58	2	13
β-strand	67-72	6	11
β-strand	76-82	7	11
α-helix	87-89	3
β-strand	91-93	3	14
β-strand	94-98	5	13
β-strand	106	1	13
β-strand	109	1	11
β-strand	111-113	3	14
β-strand	114-115	2	12

Chain Y: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-30	17
α-helix	31-33	3
α-helix	41-44	4
β-strand	57	1	8
β-strand	60	1	9
β-strand	63	1	9
β-strand	66	1	8
α-helix	75-88	14
α-helix	93-99	7
α-helix	104-135	32
α-helix	148-170	23
α-helix	178-188	11
α-helix	192-196	5
α-helix	217-235	19
β-strand	238-242	5	10
β-strand	261-265	5	10
α-helix	276-288	13
α-helix	290-292	3
α-helix	309-330	22
α-helix	335-342	8
α-helix	354-385	32
α-helix	400-420	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein translocase subunit SecA, Insertion Peptide Chimera	A	protein	836	Bacillus subtilis (strain 168), synthetic construct, Bacillus subtilis	P28366 (AlphaFold model)
Protein translocase subunit SecY	Y	protein	424	Geobacillus thermodenitrificans (strain NG80-2)	A4IJK8 (AlphaFold model)
Preprotein translocase SecE subunit	E	protein	70	Geobacillus thermodenitrificans (strain NG80-2)	A4IJH4 (AlphaFold model)
AYC08	V	protein	131	Vicugna pacos

Sequence of entity 1 (A), FASTA

>5EUL_1 Protein translocase subunit SecA, Insertion Peptide Chimera (chains A)
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDD
LLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALT
GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNEL
GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF
VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY
FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE
DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV
TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS
MEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDL
INTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAV
DSKWMDHIDAMDQLRQGIHLRGSGGSGGKKTAIAIAVALAGFATVASYAQYEDGCSGELE
RQHTFAGGPGAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEITSLEVLFQG

Sequence of entity 2 (Y), FASTA

>5EUL_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQTFGGLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYA
KRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDY
THPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYR
LTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYR
GFIK

Sequence of entity 3 (E), FASTA

>5EUL_3 Preprotein translocase SecE subunit (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE
GGHHHHHHHH

Sequence of entity 4 (V), FASTA

>5EUL_4 AYC08 (chains V)
QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKQREVVARIATDDSTMYP
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVSSGGL
PETGGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	1
TBR	Hexatantalum dodecabromide	Br12 Ta6	18
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Crystal structure of a substrate-engaged SecY protein-translocation channel. Li, L., Park, E., Ling, J. et al. Nature (2016) 531:395-399. DOI 10.1038/nature17163 · 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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