9GRC: Lipoprotein-bound LolCDE in nanodiscs

Cryo-EM structure of lipoprotein-bound LolCDE in nanodiscs. Determined by electron microscopy at 3.5 Å resolution. Released 8 Jan 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Escherichia coli K-12
Chains: 5
Atoms: 9,717
Mol. weight: 143.74 kDa
Ligands: PLM, Z41
Released: 8 Jan 2025

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

Secondary structure: helices and β-sheets

9GRC contains 46 α-helices and 51 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	23-27	5
α-helix	29-58	30
α-helix	60-62	3
β-strand	66-69	4	1
β-strand	75	1	2
α-helix	82-84	3
β-strand	90-96	7	1
β-strand	97-102	6	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	148-154	7
β-strand	161-162	2	3
β-strand	165-166	2	3
β-strand	180-181	2	3
β-strand	184-190	7	3
α-helix	195-197	3
β-strand	200-204	5	3
β-strand	219	1	2
β-strand	221-226	6	1
α-helix	232-235	4
α-helix	240-241	2
β-strand	245-248	4	1
α-helix	256-292	37
α-helix	294-303	10
α-helix	307-336	30
α-helix	362-378	17
α-helix	381-389	9
α-helix	392-395	4

Chain D: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	9
β-strand	14-16	3	10
β-strand	21-23	3	10
β-strand	31-32	2	9
β-strand	38-41	4	11
α-helix	48-55	8
β-strand	65-68	4	9
β-strand	71-72	2	9
α-helix	78-88	11
β-strand	91-92	2	11
α-helix	104-115	12
α-helix	122-133	12
α-helix	136-138	3
α-helix	152-159	8
β-strand	166-170	5	11
α-helix	183-194	12
β-strand	198-203	6	11
β-strand	219	1	12
β-strand	222	1	12

Chain E: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	23-58	36
β-strand	66-68	3	4
α-helix	78-86	9
β-strand	91-99	9	4
β-strand	104-105	2	4
β-strand	110-111	2	4
β-strand	115-118	4	4
α-helix	129-132	4
β-strand	133	1	4
β-strand	147-151	5	4
α-helix	152-158	7
β-strand	165-170	6	4
β-strand	183-193	11	4
α-helix	200-202	3
β-strand	204-207	4	4
α-helix	208-214	7
β-strand	223-228	6	4
α-helix	231-233	3
α-helix	234-241	8
β-strand	252-253	2	4
α-helix	255-297	43
α-helix	299-308	10
α-helix	312-343	32
α-helix	345-356	12
α-helix	379-394	16
α-helix	397-402	6

Chain F: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	5
β-strand	14-16	3	6
β-strand	21-23	3	6
β-strand	31-32	2	5
β-strand	38-41	4	7
α-helix	48-55	8
β-strand	65-68	4	5
β-strand	71-72	2	5
α-helix	78-88	11
β-strand	91-92	2	7
α-helix	104-108	5
α-helix	110-114	5
α-helix	126-133	8
α-helix	136-138	3
α-helix	151-159	9
β-strand	166-170	5	7
α-helix	183-194	12
β-strand	198-203	6	7
β-strand	219	1	8
β-strand	222	1	8

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	D, F	protein	241	Escherichia coli K-12	P75957 (AlphaFold model)
lipoprotein(LPP)	V	protein	10	Escherichia coli K-12	P69776 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9GRC_1 Lipoprotein-releasing system transmembrane protein LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>9GRC_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (D, F), FASTA

>9GRC_3 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Sequence of entity 4 (V), FASTA

>9GRC_4 lipoprotein(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

Primary citation

Deciphering the molecular basis of lipoprotein recognition and transport by LolCDE. Qiao, W., Shen, C., Chen, Y. et al. Signal Transduct Target Ther (2024) 9:354-354. DOI 10.1038/s41392-024-02067-w · 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

Browse structure collections

About this viewer

MolViewer shows 9GRC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.