SMTL ID : 6s8n.1

Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

2 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Covalent)(Non-covalent)

DCQ.1: 9 residues within 4Å: Chain B: I.89, F.90, R.91, M.134, G.135, Q.136 Chain D: K.78, T.81, E.82 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:K.78, D:E.82, B:Q.136 DCQ.7: 5 residues within 4Å: Chain E: T.311, S.314, F.315 Ligands: LMT.3, LMT.6 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.315

2 x LMN: Lauryl Maltose Neopentyl Glycol(Covalent)

LMN.2: 16 residues within 4Å: Chain C: M.1, R.6, I.10, S.13, L.14, V.16, L.17 Chain D: Q.293, L.297, L.300, L.304 Chain E: M.25, L.29, I.32 Ligands: L0W.4, LMN.5 11 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: C:I.10, C:L.14, C:V.16, C:L.17, C:L.17, D:L.297, D:L.300, D:L.304, E:L.29, E:I.32 Salt bridges: C:R.6 LMN.5: 13 residues within 4Å: Chain D: Q.293, G.294, V.296, L.297, L.300 Chain E: M.25, L.74, L.78, P.304, M.305, G.306, V.309 Ligands: LMN.2 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:M.25, E:L.74, E:L.78, E:V.309, D:V.296, D:L.300 Hydrogen bonds: E:Q.85, E:M.305

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 9 residues within 4Å: Chain D: M.74, R.295, V.296, M.299, M.303 Chain E: V.307, V.310 Ligands: LMT.6, DCQ.7 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:V.310, D:V.296 LMT.6: 7 residues within 4Å: Chain E: P.299, L.300, S.302, V.303, V.307 Ligands: LMT.3, DCQ.7 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.300, E:V.303, E:V.307 Hydrogen bonds: E:S.302

1 x L0W: lipopolysaccharide fragment(Non-covalent)

L0W.4: 18 residues within 4Å: Chain D: I.25, Q.29, V.32, R.33, L.307 Chain E: L.29, I.66, F.67, P.69, M.70, I.313, S.314, F.317, V.318, F.319, Y.320, V.321 Ligands: LMN.2 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:L.29, E:I.66, E:F.67, E:P.69, E:I.313, E:F.317, E:F.319, E:F.319, E:Y.320, E:V.321, D:Q.29, D:V.32, D:V.32, D:L.307, D:L.307 Salt bridges: E:K.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, X. et al., Cryo-EM structures of lipopolysaccharide transporter LptB2FGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism. Nat Commun (2019)

Release Date

2019-09-25

Peptides

Lipopolysaccharide ABC transporter, ATP-binding protein LptB: AB
Lipopolysaccharide export system protein LptC: C
Lipopolysaccharide export system permease protein LptF: D
Inner membrane protein yjgQ: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
G

Membrane

We predict this structure to be a membrane protein.
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Lipopolysaccharide ABC transporter, ATP-binding protein LptB

Lipopolysaccharide export system protein LptC

Lipopolysaccharide export system permease protein LptF

Inner membrane protein yjgQ

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