7MDY: LolCDE nucleotide-bound

LolCDE nucleotide-bound. Determined by electron microscopy at 3.5 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Escherichia coli
Chains: 4
Atoms: 9,733
Mol. weight: 141.45 kDa
Ligands: MG, AOV
Released: 11 Aug 2021

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

Secondary structure: helices and β-sheets

7MDY contains 45 α-helices and 45 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: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	29-54	26
α-helix	55-59	5
β-strand	66-69	4	4
β-strand	95-96	2	5
β-strand	99-103	5	6
β-strand	110-116	7	6
β-strand	143-145	3	6
β-strand	162-166	5	6
β-strand	172	1	7
β-strand	178	1	7
β-strand	180-186	7	6
β-strand	200-203	4	6
α-helix	207-211	5
β-strand	221-222	2	5
α-helix	229-231	3
α-helix	232-237	6
β-strand	245-248	4	4
α-helix	249-251	3
α-helix	254-292	39
α-helix	294-301	8
α-helix	307-337	31
α-helix	347-350	4
α-helix	361-365	5
α-helix	366-388	23
α-helix	392-398	7

Chain B: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
α-helix	25-58	34
β-strand	74	1	1
β-strand	78	1	1
α-helix	85-87	3
β-strand	99-103	5	2
β-strand	112-118	7	2
α-helix	138-141	4
β-strand	149-150	2	2
α-helix	154-157	4
β-strand	170	1	3
β-strand	184	1	3
β-strand	192	1	2
α-helix	200-202	3
β-strand	204-207	4	2
α-helix	210-212	3
α-helix	231-234	4
α-helix	250-252	3
α-helix	255-258	4
α-helix	262-297	36
α-helix	300-307	8
α-helix	312-343	32
α-helix	380-404	25
α-helix	407-413	7

Chains C and D: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	12
β-strand	11-15	5	13
β-strand	22-28	7	13
β-strand	37-41	5	14
α-helix	48-55	8
β-strand	66	1	12
β-strand	67	1	15
β-strand	72	1	15
α-helix	78-87	10
β-strand	89	1	14
α-helix	104-115	12
α-helix	119-133	15
α-helix	136-138	3
α-helix	148-160	13
β-strand	166-170	5	14
α-helix	178-194	17
β-strand	198-202	5	14
α-helix	209-211	3
β-strand	216-218	3	14
β-strand	223-224	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein transporter subunit LolE	B	protein	414	Escherichia coli	P75958 (AlphaFold model)
Lipo-releasing system transmembrane protein lolC	A	protein	399	Escherichia coli	P0ADC3 (AlphaFold model)
Lipoprotein-releasing system ATP-binding protein LolD	C, D	protein	236	Escherichia coli	P75957 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7MDY_1 Lipoprotein transporter subunit LolE (chains B)
MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRIL
AVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNP
QQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLM
QPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRD
AGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSG
DIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQF
LSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Sequence of entity 2 (A), FASTA

>7MDY_2 Lipo-releasing system transmembrane protein lolC (chains A)
MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNIL
GLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPA
QKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPS
QRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKL
PEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAIL
QTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAI
EPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Sequence of entity 3 (C, D), FASTA

>7MDY_3 Lipoprotein-releasing system ATP-binding protein LolD (chains C, D)
KILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDTPT
SGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPAEI
NSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARNAD
SIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSMGRLTAELSM

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
AOV	ADP orthovanadate	C10 H17 N5 O14 P2 V	2

Primary citation

Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins. Sharma, S., Zhou, R., Wan, L. et al. Nat Commun (2021) 12:4687. DOI 10.1038/s41467-021-24965-1

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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