7XHA: Protein translocase subunit SecA

Name: PDB 7XHA: Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.
Published: 2023-01-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translocase

Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-. Determined by electron microscopy at 3.35 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 3.35 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Escherichia coli
Chains: 4
Atoms: 10,102
Mol. weight: 177.03 kDa
Ligands: ADP, BEF, MG
Released: 11 Jan 2023

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

Secondary structure: helices and β-sheets

7XHA contains 59 α-helices and 30 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: 40 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16-28	13
α-helix	29-32	4
α-helix	38-52	15
α-helix	59-61	3
α-helix	62-77	16
α-helix	83-93	11
β-strand	98-99	2	1
α-helix	108-117	10
β-strand	124-128	5	2
α-helix	131-148	18
β-strand	152-154	3	2
α-helix	161-168	8
β-strand	172-176	5	2
α-helix	177-187	11
α-helix	198-201	4
β-strand	203-207	5	2
α-helix	209	1
α-helix	210-215	6
α-helix	220	1
β-strand	221-225	5	3
α-helix	232-241	10
β-strand	250-252	3	4
β-strand	259-261	3	4
α-helix	263-272	10
α-helix	284-294	11
α-helix	295-299	5
α-helix	302-305	4
β-strand	306-309	4	5
β-strand	312-315	4	5
β-strand	316	1	6
α-helix	317	1
β-strand	323	1	6
β-strand	327-329	3	3
α-helix	334-340	7
α-helix	346-348	3
β-strand	350-355	6	3
α-helix	357-361	5
β-strand	366-370	5	2
α-helix	378-384	7
α-helix	388-389	2
β-strand	390-391	2	1
β-strand	401-402	2	7
α-helix	403-405	3
α-helix	411-426	16
β-strand	432-435	4	7
α-helix	440-450	11
β-strand	457-459	3	7
α-helix	465-472	8
β-strand	480-483	4	7
β-strand	506-509	4	7
α-helix	516-526	11
β-strand	534-537	4	7
α-helix	544-549	6
α-helix	552-557	6
α-helix	558-561	4
α-helix	574-618	45
α-helix	624-642	19
α-helix	654-664	11
α-helix	681-703	23
α-helix	707-736	30
α-helix	739-744	6
α-helix	748-777	30

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	50-53	4	3

Chain E: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	19	1	8
α-helix	23-57	35

Chain Y: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	12-32	21
α-helix	43-46	4
α-helix	75-87	13
α-helix	93-100	8
α-helix	106-135	30
α-helix	147-173	27
α-helix	178-187	10
α-helix	191-201	11
α-helix	217-235	19
β-strand	238-241	4	8
β-strand	244	1	9
β-strand	262-265	4	8
α-helix	272-290	19
α-helix	295-303	9
α-helix	309-330	22
α-helix	333-343	11
β-strand	346	1	9
β-strand	347	1	10
β-strand	350	1	10
α-helix	355-389	35
α-helix	400-421	22

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 polypeptide	B	protein	303	Escherichia coli

Sequence of entity 1 (A), FASTA

>7XHA_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

>7XHA_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQQFENVGEDLFLRIVRLLLVALAVVAVIVGVIYIQQAFRK
IPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWI
RRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYV
TRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQL
VKRHYRGFIK

Sequence of entity 3 (E), FASTA

>7XHA_3 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE

Sequence of entity 4 (B), FASTA

>7XHA_4 Translocating polypeptide (chains B)
MAKKTAIAIAVALAGFATVASYAQYEDGCSGELERQHTFAGGARSIASGYYYYSGDKLPE
GVLQSGGSGSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGK
LPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEV
KFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVE
DGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHG
SAG

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
BEF	Beryllium trifluoride ion	Be F3	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
7XHB 3.33 Å, Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP
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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