9GVK: PDB entry 9GVK

Cryo-EM structure of endogenous ATP-bound LolCDE with LolD-E171Q mutations 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: 4
Atoms: 9,673
Mol. weight: 142.9 kDa
Ligands: ATP, MG
Released: 8 Jan 2025

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

Secondary structure: helices and β-sheets

9GVK contains 49 α-helices and 50 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
α-helix	21-27	7
α-helix	29-60	32
β-strand	66-68	3	1
α-helix	82-84	3
β-strand	90-96	7	1
β-strand	100-104	5	2
β-strand	109-113	5	2
β-strand	116	1	3
α-helix	122-123	2
α-helix	126-128	3
β-strand	144	1	2
β-strand	145	1	4
α-helix	148-154	7
β-strand	160-170	11	2
β-strand	179-186	8	2
α-helix	195-198	4
β-strand	200	1	2
β-strand	202	1	4
β-strand	203	1	3
β-strand	221-226	6	1
α-helix	231-234	4
β-strand	246-248	3	1
α-helix	249-251	3
α-helix	254-292	39
α-helix	294-303	10
α-helix	307-338	32
α-helix	349-350	2
α-helix	361-365	5
α-helix	367-389	23
α-helix	392-395	4

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	8
β-strand	14-16	3	9
β-strand	21-23	3	9
β-strand	28-33	6	8
β-strand	39	1	10
α-helix	48-55	8
β-strand	65-68	4	8
β-strand	71-72	2	8
α-helix	78-83	6
α-helix	84-88	5
β-strand	89-92	4	10
α-helix	104-114	11
α-helix	122-132	11
α-helix	136-138	3
α-helix	143-145	3
α-helix	148-160	13
β-strand	166-170	5	10
α-helix	178-195	18
β-strand	198-202	5	10
α-helix	206-210	5
β-strand	215	1	10

Chain E: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
α-helix	25-55	31
α-helix	56-60	5
β-strand	65	1	5
β-strand	93-94	2	5
β-strand	97	1	6
β-strand	98-105	8	7
β-strand	111-118	8	7
β-strand	150-151	2	7
α-helix	152-154	3
β-strand	167-168	2	7
β-strand	192-193	2	7
β-strand	203-207	5	7
β-strand	223	1	6
β-strand	226-227	2	5
α-helix	231-233	3
α-helix	234-241	8
α-helix	254-257	4
α-helix	259-297	39
α-helix	299-308	10
α-helix	312-343	32
α-helix	379-394	16
α-helix	397-403	7
α-helix	407-411	5

Chain F: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	11
β-strand	11	1	12
β-strand	14-16	3	13
β-strand	21-23	3	13
β-strand	28	1	12
β-strand	31-32	2	11
β-strand	38-41	4	14
α-helix	48-55	8
β-strand	65-68	4	11
β-strand	71-72	2	11
α-helix	78-87	10
β-strand	90-92	3	14
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	14
α-helix	178-195	18
β-strand	198-202	5	14
α-helix	208-211	4
β-strand	214-219	6	14
β-strand	222-224	3	14

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)

Sequence of entity 1 (C), FASTA

>9GVK_1 Lipoprotein-releasing system transmembrane protein LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 2 (E), FASTA

>9GVK_2 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 3 (D, F), FASTA

>9GVK_3 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADQPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2

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

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