7ARI: LolCDE apo structure

LolCDE apo structure. Determined by electron microscopy at 3.4 Å resolution. Released 7 Apr 2021.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Escherichia coli (strain K12)
Chains: 4
Atoms: 9,538
Mol. weight: 141.83 kDa
Released: 7 Apr 2021

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

Secondary structure: helices and β-sheets

7ARI contains 44 α-helices and 53 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 C: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
α-helix	23-54	32
β-strand	66-67	2	1
β-strand	75	1	2
β-strand	95-96	2	3
β-strand	100-104	5	4
β-strand	109-117	9	4
β-strand	143-144	2	5
β-strand	145	1	4
β-strand	146-147	2	5
α-helix	148-154	7
β-strand	160	1	5
β-strand	163-166	4	4
β-strand	180-183	4	4
β-strand	185-190	6	5
β-strand	200-204	5	4
β-strand	219	1	2
β-strand	221-222	2	3
β-strand	223-224	2	1
α-helix	233-235	3
α-helix	255-257	3
α-helix	261-265	5
α-helix	266-270	5
α-helix	274-278	5
α-helix	280-287	8
α-helix	294-302	9
α-helix	307-323	17
α-helix	326-335	10
α-helix	362-364	3
α-helix	366-379	14
α-helix	382-386	5

Chain D: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	14
β-strand	16	1	15
β-strand	21	1	15
β-strand	31-32	2	14
β-strand	39-41	3	16
α-helix	48-56	9
β-strand	67	1	17
β-strand	68	1	14
β-strand	72	1	17
α-helix	80-87	8
β-strand	89-92	4	16
α-helix	104-108	5
α-helix	110-114	5
α-helix	119-130	12
α-helix	148-157	10
β-strand	166-169	4	16
α-helix	179-194	16
β-strand	198-203	6	16
β-strand	217	1	16
β-strand	219	1	18
β-strand	222	1	18

Chain E: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	23-43	21
α-helix	45-54	10
α-helix	55-59	5
β-strand	66	1	6
α-helix	80-84	5
β-strand	96	1	7
β-strand	115-116	2	8
β-strand	147-148	2	9
β-strand	149	1	8
β-strand	150	1	9
β-strand	165-166	2	9
β-strand	187-192	6	9
β-strand	204-205	2	8
β-strand	224	1	7
β-strand	226	1	6
α-helix	254-257	4
α-helix	264-271	8
α-helix	278-283	6
α-helix	285-291	7
α-helix	293-296	4
α-helix	299-307	9
α-helix	312-342	31
α-helix	345-351	7
α-helix	379-394	16
α-helix	396-401	6

Chain F: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	10
β-strand	8-9	2	11
β-strand	31-32	2	10
β-strand	38-41	4	12
α-helix	48-56	9
β-strand	65-66	2	11
β-strand	67-68	2	13
β-strand	71-72	2	13
α-helix	84-87	4
β-strand	90-92	3	12
α-helix	104-108	5
α-helix	110-114	5
α-helix	119-130	12
α-helix	136-138	3
α-helix	153-159	7
β-strand	166-169	4	12
α-helix	179-194	16
β-strand	198-203	6	12
β-strand	217-218	2	12
β-strand	223-224	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein-releasing ABC transporter permease subunit LolC	C	protein	399	Escherichia coli (strain K12)	P0ADC3 (AlphaFold model)
Lipoprotein-releasing system transmembrane protein LolE	E	protein	414	Escherichia coli (strain K12)	P75958 (AlphaFold model)
Lipoprotein-releasing system ATP-binding protein LolD	D, F	protein	241	Escherichia coli (strain K12)	P75957 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7ARI_1 Lipoprotein-releasing ABC transporter permease subunit LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>7ARI_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (D, F), FASTA

>7ARI_3 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Primary citation

Structural basis for bacterial lipoprotein relocation by the transporter LolCDE. Tang, X., Chang, S., Zhang, K. et al. Nat Struct Mol Biol (2021) 28:347-355. DOI 10.1038/s41594-021-00573-x · PubMed

Other PDB entries of the same protein (UniProt P0ADC3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NAA 1.88 Å, Lipoprotein-releasing system transmembrane protein LolC
6F3Z 2.0 Å, Complex of E. coli LolA and periplasmic domain of LolC
6F49 2.02 Å, Periplasmic domain of LolC lacking the Hook.
9RLC 2.8 Å, LolCDE complex with Lpp lipoprotein
9XRO 2.88 Å, LolCDE in complex with SMT-738_3
9RLJ 2.9 Å, LolCDE with bound ATPgammaS
9RLD 3.0 Å, LolCDE complex with Lpp lipoprotein
9RLG 3.09 Å, LolCDE complex with LolB lipoprotein
9RLF 3.17 Å, LolCDE complex with Pal lipoprotein
9RLE 3.18 Å, LolCDE complex with Pal lipoprotein
9RLH 3.19 Å, LolCDE complex with del 9-15 LolB lipoprotein
7ARJ 3.2 Å, LolCDE in complex with lipoprotein and AMPPNP complex undimerized form

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