7ARM: LolCDE

LolCDE in complex with lipoprotein and LolA. Determined by electron microscopy at 3.6 Å resolution. Released 7 Apr 2021.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Escherichia coli (strain K12), Escherichia coli BL21(DE3)
Chains: 6
Atoms: 10,971
Mol. weight: 164.34 kDa
Ligands: PLM, Z41
Released: 7 Apr 2021

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

Secondary structure: helices and β-sheets

7ARM contains 53 α-helices and 70 β-strands across 5 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: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	17-20	4	18
β-strand	22-25	4	19
β-strand	31-35	5	19
β-strand	38-41	4	18
β-strand	47-50	4	18
β-strand	51	1	20
β-strand	57	1	20
β-strand	58	1	21
β-strand	61	1	21
β-strand	66-70	5	21
β-strand	75-79	5	21
α-helix	89-95	7
α-helix	98-100	3
β-strand	115	1	19
β-strand	124-127	4	19
β-strand	130-131	2	22
β-strand	137-139	3	22
β-strand	142-144	3	19
β-strand	148-151	4	19
β-strand	154-155	2	18
β-strand	176-177	2	21

Chain C: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	21-25	5
α-helix	29-54	26
β-strand	66	1	1
β-strand	67-69	3	2
β-strand	75	1	3
β-strand	90-96	7	1
β-strand	98-104	7	4
β-strand	109-117	9	4
β-strand	129	1	5
α-helix	134-136	3
β-strand	143-145	3	4
β-strand	147	1	5
α-helix	148-154	7
β-strand	161-166	6	4
β-strand	180-186	7	4
β-strand	190	1	5
α-helix	196-198	3
β-strand	200-204	5	4
β-strand	219	1	3
β-strand	221-226	6	1
α-helix	240-241	2
β-strand	245-247	3	2
α-helix	249-251	3
α-helix	254-270	17
α-helix	273-292	20
α-helix	294-301	8
α-helix	307-336	30
α-helix	345-347	3
α-helix	362-378	17
α-helix	381-388	8

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	13
β-strand	16	1	14
β-strand	21	1	14
β-strand	25-26	2	13
α-helix	51-54	4
β-strand	67	1	15
β-strand	72	1	15
β-strand	90-91	2	16
α-helix	104-107	4
α-helix	110-114	5
α-helix	119-121	3
α-helix	125-131	7
α-helix	143-145	3
α-helix	148-157	10
β-strand	167-168	2	16
α-helix	178-189	12
α-helix	190-192	3
β-strand	199-200	2	16
α-helix	206-208	3
β-strand	219	1	17
β-strand	222	1	17

Chain E: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	23-58	36
β-strand	67-69	3	6
α-helix	78-84	7
β-strand	91-96	6	6
β-strand	98-105	8	7
β-strand	111-118	8	7
α-helix	123-125	3
α-helix	130-132	3
β-strand	133	1	8
β-strand	147-150	4	7
α-helix	153-158	6
β-strand	165-167	3	7
α-helix	171-173	3
β-strand	186-192	7	7
β-strand	193	1	8
β-strand	204-207	4	7
α-helix	208-211	4
β-strand	222	1	7
β-strand	224-228	5	6
α-helix	236-243	8
β-strand	250-252	3	6
α-helix	259-262	4
α-helix	268-283	16
α-helix	285-297	13
α-helix	299-307	9
α-helix	312-335	24
α-helix	339-342	4
α-helix	346-352	7
α-helix	359	1
α-helix	377-401	25

Chain F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	9
β-strand	7	1	10
β-strand	14-16	3	11
β-strand	21-23	3	11
β-strand	33	1	9
β-strand	38-41	4	12
α-helix	50-54	5
β-strand	67	1	10
β-strand	72	1	10
β-strand	91-92	2	12
α-helix	104-107	4
α-helix	110-114	5
α-helix	119-128	10
α-helix	130-133	4
α-helix	148-159	12
β-strand	168-170	3	12
α-helix	179-190	12
β-strand	200-203	4	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)
LPP	V	protein	10	Escherichia coli BL21(DE3)	P69776 (AlphaFold model)
Outer-membrane lipoprotein carrier protein	A	protein	184	Escherichia coli (strain K12)	P61316

Sequence of entity 1 (C), FASTA

>7ARM_1 Lipoprotein-releasing ABC transporter permease subunit LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>7ARM_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (D, F), FASTA

>7ARM_3 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Sequence of entity 4 (V), FASTA

>7ARM_4 LPP (chains V)
CSSNAKIDQL

Sequence of entity 5 (A), FASTA

>7ARM_5 Outer-membrane lipoprotein carrier protein (chains A)
WADAASDLKSRLDKVSSFHASFTQKVTDGSGAAVQEGQGDLWVKRPNLFNWHMTQPDESI
LVSDGKTLWFYNPFVEQATATWLKDATGNTPFMLIARNQSSDWQQYNIKQNGDDFVLTPK
ASNGNLKQFTINVGRDGTIHQFSAVEQDDQRSSYQLKSQQNGAVDAAKFTFTPPQGVTVD
DQRK

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	1
Z41	(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate	C35 H68 O5	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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