6ITC: Protein translocase subunit SecA

Structure of a substrate engaged SecA-SecY protein translocation machine. Determined by electron microscopy at 3.45 Å resolution. Released 12 Jun 2019.

Method: Electron microscopy
Resolution: 3.45 Å
Organisms: Bacillus subtilis (strain 168), Geobacillus thermodenitrificans (strain NG80-2), Lama glama
Chains: 7
Atoms: 13,844
Mol. weight: 204.08 kDa
Ligands: BEF, MG, PGV, ADP
Released: 12 Jun 2019

Explore 6ITC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ITC contains 68 α-helices and 74 β-strands across 7 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, 27 β-strands

Element	Residues	Length	Sheet
α-helix	15-29	15
α-helix	30-32	3
α-helix	41-52	12
α-helix	62-77	16
α-helix	84-93	10
β-strand	97-99	3	1
α-helix	107-117	11
β-strand	125-128	4	2
α-helix	131-146	16
β-strand	153-154	2	2
α-helix	161-168	8
β-strand	173-176	4	2
α-helix	177-187	11
α-helix	193-195	3
α-helix	198-199	2
α-helix	201	1
β-strand	204-206	3	2
β-strand	207	1	3
α-helix	209	1
α-helix	210-215	6
β-strand	220-226	7	4
α-helix	232-241	10
α-helix	246-249	4
β-strand	250-253	4	5
β-strand	258-261	4	5
α-helix	263-272	10
α-helix	284-298	15
α-helix	302-305	4
β-strand	307-309	3	6
β-strand	312-314	3	6
β-strand	316	1	7
β-strand	323	1	7
α-helix	324	1
β-strand	327-329	3	8
α-helix	334-340	7
β-strand	349-356	8	4
α-helix	357-361	5
β-strand	367	1	2
β-strand	370	1	3
α-helix	375-377	3
α-helix	378-383	6
β-strand	389-391	3	1
β-strand	400	1	9
β-strand	406-407	2	10
α-helix	411-426	16
β-strand	432-435	4	11
α-helix	440-448	9
β-strand	459	1	11
α-helix	464-466	3
α-helix	467-470	4
α-helix	471-473	3
β-strand	480-483	4	11
α-helix	485-487	3
β-strand	506-508	3	11
α-helix	516-524	9
β-strand	533	1	9
β-strand	536	1	11
β-strand	538-539	2	10
α-helix	544-549	6
α-helix	572-618	47
α-helix	624-642	19
α-helix	654-664	11
α-helix	673-675	3
α-helix	681-703	23
α-helix	706-737	32
α-helix	738-742	5
α-helix	748-776	29

Chain B: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
α-helix	20-23	4
β-strand	54-56	3	8
β-strand	57	1	4

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	19-25	7	21
α-helix	29-31	3
β-strand	34-39	6	23
β-strand	47-51	5	23
β-strand	57-59	3	23
β-strand	68-72	5	21
β-strand	77-81	5	21
α-helix	84-86	3
β-strand	88-96	9	23
β-strand	98-102	3	23
β-strand	107-109	3	23
β-strand	110-111	2	22

Chain E: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-14	11
β-strand	19	1	13
α-helix	23-58	36

Chain G: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	19
β-strand	25-36	12	19
β-strand	41-48	8	19
α-helix	58-61	4
β-strand	92-100	9	19
β-strand	105-115	11	19
β-strand	118-128	11	19
β-strand	141	1	20
β-strand	148-155	8	19
β-strand	160-170	11	19
β-strand	171	1	20
β-strand	176-187	12	19
β-strand	199-208	10	19
β-strand	217-227	11	19

Chain V: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	11-12	2	16
β-strand	17-24	8	15
β-strand	34-37	4	17
β-strand	47-51	5	17
β-strand	58	1	17
β-strand	68-72	5	15
β-strand	77-83	7	15
α-helix	87-89	3
β-strand	91-94	4	17
β-strand	97	1	18
β-strand	106	1	18
β-strand	110-113	4	17
β-strand	114-115	2	16

Chain Y: 20 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	12-30	19
β-strand	35	1	12
α-helix	36	1
α-helix	41-46	6
β-strand	68	1	12
α-helix	75-87	13
α-helix	93-101	9
α-helix	104-134	31
α-helix	149-173	25
α-helix	178-187	10
α-helix	188-190	3
α-helix	191-201	11
α-helix	215-235	21
β-strand	238-242	5	13
β-strand	244	1	14
β-strand	261-265	5	13
α-helix	272-288	17
α-helix	295-303	9
α-helix	311-330	20
α-helix	333-342	10
β-strand	346	1	14
α-helix	355-380	26
α-helix	383-389	7
α-helix	400-417	18
α-helix	420-423	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein translocase subunit SecA	A	protein	780	Bacillus subtilis (strain 168)	P28366 (AlphaFold model)
Protein translocase subunit SecY	Y	protein	424	Geobacillus thermodenitrificans (strain NG80-2)	A4IJK8 (AlphaFold model)
Protein translocase subunit SecE	E	protein	70	Geobacillus thermodenitrificans (strain NG80-2)	A4IJH4 (AlphaFold model)
Nanobody	V	protein	116	Lama glama
Translocating peptide	B	protein	59	Escherichia coli	P0A910 (AlphaFold model)
Green fluorescent protein	G	protein	236	Aequorea victoria	P42212
Nanobody	C	protein	112	Lama glama

Sequence of entity 1 (A), FASTA

>6ITC_1 Protein translocase subunit SecA (chains A)
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDD
LLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALT
GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNEL
GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF
VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY
FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE
DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV
TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS
MEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDL
INTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAV
DSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEI

Sequence of entity 2 (Y), FASTA

>6ITC_2 Protein translocase subunit SecY (chains Y)
MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFC
GGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVL
GFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGIS
IIIFAGIVSGIPTILNQIYAQTFGGLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYA
KRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDY
THPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYR
LTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYR
GFIK

Sequence of entity 3 (E), FASTA

>6ITC_3 Protein translocase subunit SecE (chains E)
MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFE
GGHHHHHHHH

Sequence of entity 4 (V), FASTA

>6ITC_4 Nanobody (chains V)
QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKRREVVARIATDDSTMYP
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVS

Sequence of entity 5 (B), FASTA

>6ITC_5 Translocating peptide (chains B)
MAKKTAIAIAVALAGFATVASYAQYEDGCSGELERQHTFAGGARSISGDGDSPHSYHSG

Sequence of entity 6 (G), FASTA

>6ITC_6 Green fluorescent protein (chains G)
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL
VTTFXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNR
IELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHY
QQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK

Sequence of entity 7 (C), FASTA

>6ITC_7 Nanobody (chains C)
VALVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSAGDRSSYED
SVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVS

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	1
MG	Magnesium ion	Mg	1
PGV	(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H77 O10 P	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Structure of the substrate-engaged SecA-SecY protein translocation machine. Ma, C., Wu, X., Sun, D. et al. Nat Commun (2019) 10:2872-2872. DOI 10.1038/s41467-019-10918-2 · 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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