7ARJ: LolCDE

LolCDE in complex with lipoprotein and AMPPNP complex undimerized form. 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: 9,601
Mol. weight: 144.8 kDa
Ligands: PLM, Z41, MG, ANP
Released: 7 Apr 2021

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

Secondary structure: helices and β-sheets

7ARJ contains 51 α-helices and 60 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: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	23-27	5
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	98-104	7	3
β-strand	111-117	7	3
β-strand	129	1	3
α-helix	134-136	3
β-strand	143-147	5	3
α-helix	148-152	5
β-strand	161-166	6	3
α-helix	170-172	3
β-strand	180-190	11	3
β-strand	202-204	3	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	256-270	15
α-helix	273-292	20
α-helix	295-303	9
α-helix	307-311	5
α-helix	313-317	5
α-helix	320-338	19
α-helix	362-378	17
α-helix	381-388	8

Chain D: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	16
β-strand	13-16	4	17
β-strand	21-25	5	17
β-strand	31-32	2	16
β-strand	38-41	4	18
α-helix	48-54	7
β-strand	67-68	2	16
α-helix	84-87	4
β-strand	89-91	3	18
α-helix	104-108	5
α-helix	110-114	5
α-helix	122-124	3
β-strand	166-168	3	18
α-helix	181-183	3
α-helix	190-192	3
β-strand	199-203	5	18
β-strand	216-217	2	18

Chain E: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	22-24	3
α-helix	26-58	33
β-strand	66-69	4	4
β-strand	75	1	5
α-helix	80-83	4
β-strand	91-97	7	4
β-strand	98-99	2	6
β-strand	103-104	2	7
β-strand	112	1	7
β-strand	115-118	4	6
α-helix	123-125	3
α-helix	129-131	3
β-strand	133	1	8
β-strand	147-148	2	9
β-strand	149-150	2	6
β-strand	151	1	8
α-helix	152-158	7
β-strand	165-166	2	9
β-strand	168-170	3	7
α-helix	181-182	2
β-strand	183-184	2	7
β-strand	187-189	3	9
β-strand	193	1	8
β-strand	204-207	4	6
α-helix	208-214	7
β-strand	221	1	5
β-strand	223-228	6	4
α-helix	240-242	3
β-strand	250-252	3	4
α-helix	255-258	4
α-helix	261-267	7
α-helix	268-270	3
α-helix	272-283	12
α-helix	285-297	13
α-helix	299-308	10
α-helix	312-343	32
α-helix	345-356	12
α-helix	378-394	17
α-helix	397-401	5

Chain F: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	10
β-strand	9	1	11
β-strand	16	1	12
β-strand	21	1	12
β-strand	31-32	2	10
β-strand	37-38	2	13
β-strand	41	1	14
α-helix	48-54	7
β-strand	65	1	11
β-strand	68	1	10
β-strand	71	1	10
α-helix	78-87	10
β-strand	89-92	4	13
α-helix	104-108	5
α-helix	110-114	5
α-helix	122-133	12
α-helix	148-159	12
β-strand	166-170	5	13
α-helix	178-183	6
α-helix	185-190	6
β-strand	199-202	4	13
β-strand	214	1	13
β-strand	217	1	14
β-strand	219	1	15
β-strand	222	1	15

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

>7ARJ_1 Lipoprotein-releasing ABC transporter permease subunit LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>7ARJ_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (D, F), FASTA

>7ARJ_3 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Sequence of entity 4 (V), FASTA

>7ARJ_4 LPP (chains V)
CSSNAKIDQL

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
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

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
7ARL 3.2 Å, LolCDE in complex with lipoprotein and ADP

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