6F49: Periplasmic domain of LolC lacking the Hook

Periplasmic domain of LolC lacking the Hook. Determined by X-ray diffraction at 2.02 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 2.02 Å
Organisms: Escherichia coli (strain K12), Escherichia coli
Chains: 4
Atoms: 7,175
Mol. weight: 98.8 kDa
Ligands: PG5
Released: 25 Jul 2018

Explore 6F49 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F49 contains 49 α-helices and 52 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 A: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	49-58	10
α-helix	60-62	3
β-strand	66-70	5	1
β-strand	75	1	2
α-helix	82-84	3
β-strand	90-96	7	1
β-strand	97-104	8	3
β-strand	109-117	9	3
α-helix	126-128	3
β-strand	129-130	2	3
α-helix	134-136	3
β-strand	143-147	5	3
α-helix	148-154	7
β-strand	161-166	6	3
β-strand	180-190	11	3
α-helix	195-198	4
β-strand	200-204	5	3
α-helix	205-211	7
α-helix	214-215	2
β-strand	219	1	2
β-strand	221-226	6	1
α-helix	229-231	3
α-helix	232-235	4
β-strand	244-248	5	1
α-helix	250-265	16

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	49-58	10
α-helix	60-62	3
β-strand	66-70	5	4
β-strand	75	1	5
α-helix	82-84	3
β-strand	90-96	7	4
β-strand	97-104	8	6
β-strand	109-117	9	6
α-helix	126-128	3
β-strand	129-130	2	6
α-helix	134-136	3
β-strand	143-147	5	6
α-helix	148-154	7
β-strand	161-166	6	6
β-strand	180-190	11	6
α-helix	195-198	4
β-strand	200-204	5	6
α-helix	205-211	7
α-helix	214-215	2
β-strand	219	1	5
β-strand	221-226	6	4
α-helix	229-231	3
α-helix	232-235	4
β-strand	244-248	5	4
α-helix	250-266	17

Chain C: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	49-58	10
α-helix	60-62	3
β-strand	66-70	5	7
β-strand	75	1	8
α-helix	82-84	3
β-strand	90-96	7	7
β-strand	97-104	8	9
β-strand	109-117	9	9
α-helix	126-128	3
β-strand	129-130	2	9
α-helix	134-136	3
β-strand	143-147	5	9
α-helix	148-154	7
β-strand	161-166	6	9
β-strand	180-190	11	9
α-helix	195-198	4
β-strand	200-204	5	9
α-helix	205-211	7
α-helix	214-215	2
β-strand	219	1	8
β-strand	221-226	6	7
α-helix	229-231	3
α-helix	232-235	4
β-strand	244-248	5	7
α-helix	250-267	18

Chain D: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	49-58	10
α-helix	60-62	3
β-strand	66-70	5	10
β-strand	75	1	11
α-helix	82-84	3
β-strand	90-96	7	10
β-strand	97-104	8	12
β-strand	109-117	9	12
α-helix	122-123	2
α-helix	126-128	3
β-strand	129-130	2	12
α-helix	134-136	3
β-strand	143-147	5	12
α-helix	148-154	7
β-strand	161-166	6	12
β-strand	180-190	11	12
α-helix	195-198	4
β-strand	200-204	5	12
α-helix	205-211	7
α-helix	214-215	2
β-strand	219	1	11
β-strand	221-226	6	10
α-helix	229-231	3
α-helix	232-235	4
β-strand	244-248	5	10
α-helix	250-267	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane…	A, B, C, D	protein	219	Escherichia coli (strain K12), Escherichia coli	P0ADC3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6F49_1 Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC (chains A, B, C, D)
MNGFERELQNNILGLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSAR
SVAVGVMLGIDPAQKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVG
ASQRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQ
KLPEGSKWQDWRDRKGELFQAVRMEKNMAAALEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PG5	1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane	C8 H18 O4	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Insights into bacterial lipoprotein trafficking from a structure of LolA bound to the LolC periplasmic domain. Kaplan, E., Greene, N.P., Crow, A. et al. Proc Natl Acad Sci U S A (2018) 115:E7389-E7397. DOI 10.1073/pnas.1806822115 · 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
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

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