7V8L: LolCDE with bound RcsF in nanodiscs

LolCDE with bound RcsF in nanodiscs. Determined by electron microscopy at 3.5 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Escherichia coli K-12
Chains: 5
Atoms: 9,505
Mol. weight: 153.03 kDa
Ligands: PCJ
Released: 21 Sept 2022

Explore 7V8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V8L contains 57 α-helices and 44 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: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
α-helix	23-27	5
α-helix	29-58	30
α-helix	60-62	3
β-strand	66-70	5	3
β-strand	75	1	4
α-helix	82-84	3
β-strand	90-96	7	3
β-strand	97-104	8	5
β-strand	109-117	9	5
α-helix	126-128	3
β-strand	129-130	2	5
α-helix	134-136	3
β-strand	143-147	5	5
α-helix	148-154	7
β-strand	161-173	13	5
β-strand	176-190	15	5
α-helix	195-198	4
β-strand	200-204	5	5
α-helix	205-211	7
α-helix	214-215	2
β-strand	219	1	4
β-strand	221-226	6	3
α-helix	229-231	3
α-helix	232-235	4
β-strand	244-248	5	3
α-helix	250-270	21
α-helix	272-302	31
α-helix	307-336	30
α-helix	340-343	4
α-helix	362-389	28
α-helix	392-396	5

Chain D: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	6
β-strand	39-41	3	7
α-helix	49-55	7
β-strand	63-68	6	6
β-strand	71-72	2	6
α-helix	78-83	6
α-helix	84-88	5
β-strand	89-91	3	7
α-helix	104-114	11
α-helix	119-133	15
α-helix	143-145	3
α-helix	148-159	12
β-strand	166-170	5	7
α-helix	178-190	13
α-helix	191-195	5
β-strand	198-202	5	7
α-helix	206-210	5
β-strand	214-219	6	7
β-strand	222-228	7	7

Chain E: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-15	7
α-helix	25-54	30
α-helix	55-59	5
β-strand	66-69	4	1
α-helix	78-86	9
β-strand	91-97	7	1
β-strand	98-106	9	2
β-strand	109-117	9	2
α-helix	120-126	7
α-helix	129-132	4
β-strand	133	1	2
β-strand	147-151	5	2
α-helix	152-157	6
β-strand	165-170	6	2
α-helix	177-179	3
β-strand	183-193	11	2
α-helix	199-201	3
β-strand	204-206	3	2
α-helix	208-215	8
β-strand	223-228	6	1
α-helix	234-244	11
β-strand	250-253	4	1
α-helix	254-297	44
α-helix	299-306	8
α-helix	314-340	27
α-helix	345-355	11
α-helix	377-403	27
α-helix	407-411	5

Chain F: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	8
β-strand	38-41	4	9
α-helix	49-55	7
β-strand	63-68	6	8
β-strand	71-72	2	8
α-helix	78-83	6
α-helix	84-88	5
β-strand	89-92	4	9
α-helix	104-114	11
α-helix	119-133	15
α-helix	135-137	3
α-helix	148-159	12
β-strand	166-170	5	9
α-helix	178-190	13
α-helix	191-195	5
β-strand	198-202	5	9
α-helix	206-209	4
β-strand	214-217	4	9
β-strand	219	1	10
β-strand	222	1	10
β-strand	226-228	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein-releasing system transmembrane protein LolE	E	protein	414	Escherichia coli K-12	P75958 (AlphaFold model)
Outer membrane lipoprotein RcsF	A	protein	118	Escherichia coli K-12	P69411 (AlphaFold model)
Lipoprotein-releasing system transmembrane protein LolC	C	protein	399	Escherichia coli K-12	P0ADC3 (AlphaFold model)
Lipoprotein-releasing system ATP-binding protein LolD	D, F	protein	233	Escherichia coli K-12	P75957 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>7V8L_1 Lipoprotein-releasing system transmembrane protein LolE (chains E)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 2 (A), FASTA

>7V8L_2 Outer membrane lipoprotein RcsF (chains A)
SMLSRSPVEPVQSTAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQA
SNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSALNITAK

Sequence of entity 3 (C), FASTA

>7V8L_3 Lipoprotein-releasing system transmembrane protein LolC (chains C)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 4 (D, F), FASTA

>7V8L_4 Lipoprotein-releasing system ATP-binding protein LolD (chains D, F)
MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDT
PTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPA
EINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARN
ADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAE

Ligands and cofactors

ID	Name	Formula	Copies
PCJ	(2R)-3-{[(2S)-3-hydroxy-2-(palmitoylamino)propyl]thio}propane-1,2-diyl…	C54 H105 N O6 S	1

Primary citation

Cryo-EM structures of LolCDE reveal the molecular mechanism of bacterial lipoprotein sorting in Escherichia coli. Bei, W., Luo, Q., Shi, H. et al. PLoS Biol (2022) 20:e3001823-e3001823. DOI 10.1371/journal.pbio.3001823 · PubMed

Other PDB entries of the same protein (UniProt P75958 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
7ARL 3.2 Å, LolCDE in complex with lipoprotein and ADP
9RLK 3.29 Å, LolCDE(delta 235-252) complex with Pal lipoprotein
7ARH 3.3 Å, LolCDE in complex with lipoprotein

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