2IBM: Preprotein translocase secA subunit

A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA. Determined by X-ray diffraction at 3.2 Å resolution. Released 14 Nov 2006.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Bacillus subtilis
Chains: 2
Atoms: 12,403
Mol. weight: 178.26 kDa
Ligands: ADP
Released: 14 Nov 2006

Explore 2IBM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IBM contains 83 α-helices and 43 β-strands across 2 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: 42 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	15-28	14
α-helix	29-31	3
α-helix	38-54	17
α-helix	59-61	3
α-helix	62-76	15
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	152-155	4	1
α-helix	163-169	7
β-strand	172-176	5	1
α-helix	177-187	11
β-strand	203-207	5	1
α-helix	209-210	2
α-helix	211-215	5
α-helix	216-218	3
α-helix	220	1
β-strand	221-224	4	2
α-helix	230-237	8
α-helix	238-241	4
α-helix	263-271	9
α-helix	284-297	14
β-strand	308	1	3
β-strand	314	1	3
β-strand	316	1	4
β-strand	323	1	4
α-helix	328-329	2
α-helix	334-335	2
α-helix	336-340	5
β-strand	351-355	5	2
α-helix	357-362	6
β-strand	366-371	6	1
α-helix	378-381	4
α-helix	388	1
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	411-428	18
β-strand	432-436	5	5
α-helix	439-451	13
β-strand	457-459	3	5
α-helix	464-472	9
α-helix	473-475	3
β-strand	480-484	5	5
α-helix	500-502	3
β-strand	506-509	4	5
α-helix	516-524	9
α-helix	528-530	3
β-strand	534-537	4	5
β-strand	538-540	3	6
α-helix	547-549	3
β-strand	552-554	3	7
α-helix	572-618	47
α-helix	625-642	18
α-helix	656-660	5
α-helix	661-665	5
α-helix	683-702	20
α-helix	707-718	12
α-helix	719-724	6
α-helix	725-735	11
α-helix	749-776	28

Chain B: 41 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	13-28	16
α-helix	30-33	4
α-helix	43-54	12
α-helix	58-76	19
α-helix	83-93	11
β-strand	97-98	2	8
α-helix	106-119	14
β-strand	124-128	5	8
α-helix	131-148	18
β-strand	152-155	4	8
α-helix	161-168	8
β-strand	172-176	5	8
α-helix	177-187	11
β-strand	203-207	5	8
α-helix	209-210	2
α-helix	211-215	5
β-strand	220-224	5	7
α-helix	233-242	10
α-helix	263-272	10
β-strand	280	1	9
α-helix	281-283	3
α-helix	284-294	11
α-helix	295-299	5
β-strand	306-309	4	10
β-strand	312-317	6	10
β-strand	322-324	3	10
α-helix	333-341	9
β-strand	353-356	4	7
α-helix	357-361	5
β-strand	366-370	5	8
α-helix	378-380	3
α-helix	381-385	5
β-strand	389-390	2	8
α-helix	392-394	3
β-strand	401-408	8	11
α-helix	411-428	18
β-strand	432-436	5	11
α-helix	439-445	7
α-helix	449-452	4
β-strand	457-459	3	11
α-helix	464-472	9
α-helix	473-475	3
β-strand	480-484	5	11
α-helix	494-496	3
α-helix	500-502	3
β-strand	505-509	5	11
α-helix	516-523	8
β-strand	533-540	8	11
α-helix	554-559	6
β-strand	569	1	11
α-helix	572-617	46
α-helix	622-624	3
α-helix	627-645	19
α-helix	655-662	8
α-helix	673-676	4
α-helix	681-702	22
α-helix	707-718	12
α-helix	719-724	6
α-helix	725-737	13
α-helix	738-740	3
α-helix	749-776	28
β-strand	779	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Preprotein translocase secA subunit	A, B	protein	780	Bacillus subtilis	P28366 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2IBM_1 Preprotein translocase secA subunit (chains A, B)
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDD
LLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALT
GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNEL
GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF
VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY
FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE
DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV
TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS
MEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDL
INTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAV
DSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEI

Ligands and cofactors

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

Primary citation

A Novel Dimer Interface and Conformational Changes Revealed by an X-ray Structure of B. subtilis SecA. Zimmer, J., Li, W., Rapoport, T.A. J Mol Biol (2006) 364:259-265. DOI 10.1016/j.jmb.2006.08.044 · 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
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
8Y9Z 3.41 Å, Structure of the SecA-SecY complex with the substrate HmBRI-3TM

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