7ARL: LolCDE

LolCDE in complex with lipoprotein and ADP. Determined by electron microscopy at 3.2 Å resolution. Released 7 Apr 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Escherichia coli (strain K12), Escherichia coli K-12
Chains: 5
Atoms: 9,467
Mol. weight: 144.64 kDa
Ligands: Z41, ADP, MG, PLM
Released: 7 Apr 2021

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

Secondary structure: helices and β-sheets

7ARL contains 48 α-helices and 73 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	21-27	7
α-helix	29-55	27
α-helix	56-60	5
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	93-96	4	1
β-strand	98-99	2	3
β-strand	102-104	3	3
β-strand	111	1	3
β-strand	113-117	5	3
β-strand	129	1	4
β-strand	143-145	3	3
α-helix	148-154	7
β-strand	161-166	6	3
β-strand	173	1	5
β-strand	176	1	5
β-strand	180-188	9	3
β-strand	190	1	4
α-helix	196-198	3
β-strand	200-204	5	3
β-strand	219	1	2
β-strand	221-224	4	1
α-helix	240-241	2
β-strand	245-247	3	1
α-helix	249-251	3
α-helix	257-270	14
α-helix	273-292	20
α-helix	294-303	10
α-helix	307-310	4
α-helix	313-338	26
α-helix	362-378	17
α-helix	381-389	9

Chain D: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	20
β-strand	12	1	21
β-strand	14	1	22
β-strand	23	1	22
β-strand	29-32	4	20
β-strand	37-38	2	23
β-strand	41	1	24
α-helix	53-56	4
β-strand	63	1	21
β-strand	67-68	2	20
β-strand	71-72	2	20
α-helix	78-84	7
β-strand	89-92	4	23
α-helix	104-108	5
α-helix	110-114	5
α-helix	122-133	12
α-helix	152-159	8
β-strand	166-169	4	23
α-helix	181-188	8
β-strand	198-200	3	23
β-strand	214	1	23
β-strand	217	1	24
β-strand	218-219	2	25
β-strand	222-223	2	25

Chain E: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
α-helix	26-34	9
α-helix	39-58	20
β-strand	67-69	3	6
β-strand	75	1	7
α-helix	83-86	4
β-strand	91-96	6	6
β-strand	99	1	8
β-strand	102-103	2	9
β-strand	104	1	10
β-strand	112-113	2	9
β-strand	115-116	2	8
α-helix	130-132	3
β-strand	133	1	11
β-strand	148	1	12
β-strand	149-150	2	8
α-helix	152-158	7
β-strand	165-170	6	10
α-helix	181-182	2
β-strand	183-188	6	10
β-strand	189	1	12
β-strand	193	1	11
β-strand	204-205	2	8
α-helix	208-211	4
β-strand	221	1	7
β-strand	224-228	5	6
β-strand	250-252	3	6
α-helix	255-258	4
α-helix	260-267	8
α-helix	272-283	12
α-helix	285-289	5
α-helix	293-296	4
α-helix	299-308	10
α-helix	312-315	4
α-helix	318-323	6
α-helix	325-343	19
α-helix	346-352	7
α-helix	378-403	26

Chain F: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	13
β-strand	12	1	14
β-strand	13-17	5	15
β-strand	20-25	6	15
β-strand	32	1	13
β-strand	38	1	16
β-strand	41	1	17
β-strand	44	1	18
β-strand	46	1	18
α-helix	51-56	6
β-strand	63	1	14
β-strand	67-68	2	13
β-strand	71-72	2	13
α-helix	78-87	10
β-strand	89-92	4	16
α-helix	104-108	5
α-helix	110-114	5
α-helix	119-131	13
α-helix	150-158	9
β-strand	166-170	5	16
α-helix	181-194	14
β-strand	199-202	4	16
β-strand	203	1	17
β-strand	217	1	17
β-strand	218-219	2	19
β-strand	222-223	2	19

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)
LPP	V	protein	10	Escherichia coli K-12	P69776 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7ARL_1 Lipoprotein-releasing ABC transporter permease subunit LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>7ARL_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (D, F), FASTA

>7ARL_3 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Sequence of entity 4 (V), FASTA

>7ARL_4 LPP (chains V)
CSSNAKIDQL

Ligands and cofactors

ID	Name	Formula	Copies
Z41	(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate	C35 H68 O5	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2
PLM	Palmitic acid	C16 H32 O2	1

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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