9XRO: LolCDE

LolCDE in complex with SMT-738_3. Determined by electron microscopy at 2.88 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 2.88 Å
Organism: Escherichia coli K-12
Chains: 3
Atoms: 7,230
Mol. weight: 115.65 kDa
Ligands: A1ER4
Released: 18 Mar 2026

Explore 9XRO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XRO contains 41 α-helices and 40 β-strands across 3 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	29-56	28
α-helix	59-62	4
β-strand	66-69	4	1
β-strand	70	1	2
β-strand	75	1	3
α-helix	82-84	3
β-strand	90-96	7	1
β-strand	97-104	8	4
β-strand	109-117	9	4
α-helix	126-128	3
β-strand	129-130	2	4
α-helix	134-136	3
β-strand	143-147	5	4
α-helix	148-154	7
β-strand	161-172	12	4
β-strand	177-190	14	4
α-helix	195-198	4
β-strand	200-204	5	4
α-helix	205-211	7
α-helix	214-215	2
β-strand	219	1	3
β-strand	221-226	6	1
α-helix	232-235	4
α-helix	240-241	2
β-strand	244	1	2
β-strand	247-248	2	1
α-helix	250-283	34
α-helix	284-288	5
α-helix	294-297	4
α-helix	307-338	32
α-helix	362-385	24

Chain E: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	25-54	30
α-helix	55-59	5
α-helix	60-62	3
β-strand	66-69	4	5
β-strand	70	1	6
α-helix	78-86	9
β-strand	91-101	11	5
β-strand	103-106	4	5
β-strand	109-111	3	5
β-strand	114-118	5	5
α-helix	120-124	5
α-helix	130-132	3
β-strand	133	1	5
β-strand	147-151	5	5
α-helix	152-158	7
β-strand	165-169	5	5
β-strand	184-193	10	5
β-strand	203-207	5	5
α-helix	208-215	8
β-strand	223-228	6	5
α-helix	231-233	3
α-helix	234-244	11
β-strand	249	1	6
β-strand	252-253	2	5
α-helix	254-257	4
α-helix	259-291	33
α-helix	298-307	10
α-helix	319-343	25
α-helix	345-348	4
α-helix	377-402	26

Chain F: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	7
β-strand	14	1	8
β-strand	23	1	8
β-strand	28-33	6	7
β-strand	38-42	5	9
α-helix	48-55	8
β-strand	63-68	6	7
β-strand	71-72	2	7
α-helix	78-88	11
β-strand	89-92	4	9
α-helix	104-114	11
α-helix	119-132	14
α-helix	136-138	3
α-helix	143-145	3
α-helix	148-160	13
β-strand	166-170	5	9
α-helix	178-194	17
β-strand	198-202	5	9
β-strand	214-218	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein-releasing system transmembrane protein LolC	C	protein	399	Escherichia coli K-12	P0ADC3 (AlphaFold model)
Lipoprotein-releasing system transmembrane protein LolE	E	protein	414	Escherichia coli K-12	P75958 (AlphaFold model)
Lipoprotein-releasing system ATP-binding protein LolD	F	protein	241	Escherichia coli K-12	P75957 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9XRO_1 Lipoprotein-releasing system transmembrane protein LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>9XRO_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (F), FASTA

>9XRO_3 Lipoprotein-releasing system ATP-binding protein LolD (chains F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
A1ER4	2-azanyl-1-[6-[2-azanyl-5-(3-methylpyridin-4-yl)-1H-imidazol-4-yl]-2,3-dihydro-…	C21 H24 N6 O2	1

Primary citation

Molecular mechanism of action of small molecule SMT-738 on bacterial lipoprotein transporter LolCDE. Li, H., Zhu, X., Zhang, D. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-69411-2 · 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
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
7ARL 3.2 Å, LolCDE in complex with lipoprotein and ADP

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