7XHB: SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP

Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP. Determined by electron microscopy at 3.33 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 3.33 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Escherichia coli
Chains: 4
Atoms: 10,122
Mol. weight: 181.17 kDa
Ligands: ADP, MG
Released: 11 Jan 2023

Explore 7XHB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XHB contains 59 α-helices and 34 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: 35 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	15-32	18
α-helix	38-53	16
α-helix	62-77	16
α-helix	83-93	11
β-strand	97-99	3	1
α-helix	107-118	12
β-strand	123-128	6	2
α-helix	131-145	15
β-strand	152	1	2
α-helix	161-168	8
β-strand	172-176	5	2
α-helix	177-187	11
β-strand	201-206	6	2
α-helix	209-210	2
α-helix	211-215	5
β-strand	221-225	5	3
α-helix	232-241	10
β-strand	246	1	4
β-strand	250-251	2	4
β-strand	260-261	2	4
α-helix	263-272	10
α-helix	284-294	11
α-helix	295-299	5
α-helix	302-305	4
β-strand	306-308	3	5
β-strand	313-316	4	5
β-strand	323-324	2	5
β-strand	327-329	3	3
α-helix	334-340	7
β-strand	350-355	6	3
α-helix	357-362	6
β-strand	366-367	2	2
β-strand	371	1	1
α-helix	376-384	9
β-strand	389-391	3	1
α-helix	392-394	3
β-strand	401-402	2	6
α-helix	403-405	3
β-strand	406-407	2	7
α-helix	411-428	18
β-strand	432-435	4	6
α-helix	439-451	13
β-strand	457-459	3	6
α-helix	464-466	3
α-helix	467-473	7
β-strand	480-483	4	6
β-strand	505-509	5	6
α-helix	516-523	8
β-strand	533-537	5	6
β-strand	539	1	7
α-helix	544-548	5
α-helix	552-558	7
β-strand	569-570	2	7
α-helix	572-619	48
α-helix	624-642	19
α-helix	654-664	11
α-helix	674-676	3
α-helix	681-700	20
α-helix	706-737	32
α-helix	738-744	7
α-helix	748-776	29

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	48-53	6	3

Chain E: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	15-17	3
β-strand	19	1	8
α-helix	20-22	3
α-helix	23-58	36

Chain Y: 19 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
α-helix	12-33	22
α-helix	41-47	7
α-helix	75-86	12
α-helix	93-100	8
α-helix	104-135	32
α-helix	149-172	24
α-helix	178-188	11
α-helix	191-202	12
α-helix	215-235	21
β-strand	238-241	4	8
β-strand	244	1	9
β-strand	262-265	4	8
α-helix	272-282	11
α-helix	284-287	4
α-helix	295-303	9
α-helix	309-330	22
α-helix	333-342	10
β-strand	346	1	9
β-strand	347	1	10
β-strand	350	1	10
α-helix	355-380	26
α-helix	383-386	4
α-helix	400-416	17
α-helix	420-423	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein translocase subunit SecA	A	protein	778	Bacillus subtilis subsp. subtilis str. 168	P28366 (AlphaFold model)
Protein translocase subunit SecY	Y	protein	430	Geobacillus thermodenitrificans NG80-2	A4IJK8 (AlphaFold model)
Protein translocase subunit SecE	E	protein	60	Geobacillus thermodenitrificans NG80-2	A4IJH4 (AlphaFold model)
Translocating peptide	B	protein	345	Escherichia coli

Sequence of entity 1 (A), FASTA

>7XHB_1 Protein translocase subunit SecA (chains A)
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDD
LLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALT
GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNEL
GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF
VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY
FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE
DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV
TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS
MEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDL
INTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAV
DSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA

Sequence of entity 2 (Y), FASTA

>7XHB_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQQFENVGEDLFLRIVRLLLVALAVVAVIVGVIYIQQAFRK
IPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWI
RRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYV
TRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQL
VKRHYRGFIK

Sequence of entity 3 (E), FASTA

>7XHB_3 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE

Sequence of entity 4 (B), FASTA

>7XHB_4 Translocating peptide (chains B)
MAKKTAIAIAVALAGFATVASYAQYEDGCSGELERQHTFAGGARSIASGYYYYSGDKLPE
GVLQSGGSGSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGK
LPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEV
KFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVE
DGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHG
SAGLEVLFQGPANGGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Structural basis of SecA-mediated protein translocation. Dong, L., Yang, S., Chen, J. et al. Proc Natl Acad Sci U S A (2023) 120:e2208070120-e2208070120. DOI 10.1073/pnas.2208070120 · 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
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
8Y9Z 3.41 Å, Structure of the SecA-SecY complex with the substrate HmBRI-3TM

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