SMTL ID : 7duw.1

Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with two lysyl-phosphatidylglycerol molecules

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

LMT.1: 10 residues within 4Å: Chain A: I.47, Y.56, V.59, L.63, T.64, V.301, V.482, V.483, F.486 Ligands: EV9.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.47, A:V.59, A:L.63, A:V.301, A:V.301, A:V.482, A:V.483, A:F.486, A:F.486 Hydrogen bonds: A:Y.56, A:L.63 LMT.8: 10 residues within 4Å: Chain B: I.47, Y.56, V.59, L.63, T.64, V.301, V.482, V.483, F.486 Ligands: EV9.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.47, B:V.59, B:L.63, B:V.301, B:V.301, B:V.482, B:V.483, B:F.486, B:F.486 Hydrogen bonds: B:Y.56, B:L.63

4 x EV9: [(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate(Non-covalent)

EV9.2: 23 residues within 4Å: Chain A: S.81, Y.113, G.116, N.117, T.152, F.155, G.156, A.160, G.163, A.164, L.167, I.192, D.234, S.238, Y.260, A.261, I.262, V.264, G.265, V.268, L.269, H.271, Y.307 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.155, A:L.167, A:V.264, A:V.268 Hydrogen bonds: A:S.81, A:N.117, A:S.238, A:S.238 Salt bridges: A:H.271 EV9.3: 27 residues within 4Å: Chain A: F.40, A.44, I.47, V.60, T.118, P.273, A.274, F.276, E.280, L.297, V.301, R.304, V.305, N.308, L.354, M.357, M.358, F.361, S.362, P.368, A.433, I.434, V.435, E.436, L.439, G.479 Ligands: LMT.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.40, A:F.40, A:A.44, A:P.273, A:A.274, A:F.276, A:F.276, A:F.276, A:F.276, A:F.276, A:E.280, A:L.297, A:V.301, A:R.304, A:L.354, A:M.358, A:F.361, A:P.368, A:L.439 Hydrogen bonds: A:S.362, A:I.434, A:V.435, A:E.436, A:E.436, A:E.436 EV9.9: 23 residues within 4Å: Chain B: S.81, Y.113, G.116, N.117, T.152, F.155, G.156, A.160, G.163, A.164, L.167, I.192, D.234, S.238, Y.260, A.261, I.262, V.264, G.265, V.268, L.269, H.271, Y.307 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.155, B:L.167, B:V.264, B:V.268 Hydrogen bonds: B:S.81, B:N.117, B:S.238, B:S.238 Salt bridges: B:H.271 EV9.10: 27 residues within 4Å: Chain B: F.40, A.44, I.47, V.60, T.118, P.273, A.274, F.276, E.280, L.297, V.301, R.304, V.305, N.308, L.354, M.357, M.358, F.361, S.362, P.368, A.433, I.434, V.435, E.436, L.439, G.479 Ligands: LMT.8 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.40, B:F.40, B:A.44, B:P.273, B:A.274, B:F.276, B:F.276, B:F.276, B:F.276, B:F.276, B:E.280, B:L.297, B:V.301, B:R.304, B:L.354, B:M.358, B:F.361, B:P.368, B:L.439 Hydrogen bonds: B:S.362, B:I.434, B:V.435, B:E.436, B:E.436, B:E.436

2 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.4: 15 residues within 4Å: Chain A: K.67, S.69, L.72, L.73, L.75, L.76, F.77, G.79, L.80, F.233 Chain B: L.168, I.190, L.193 Ligands: J4U.7, PGT.12 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.72, A:L.73, A:F.77, A:F.77, A:L.80, A:F.233, B:L.168, B:L.193 Hydrogen bonds: A:S.69 Salt bridges: A:K.67 LHG.11: 15 residues within 4Å: Chain A: L.168, I.190, L.193 Chain B: K.67, S.69, L.72, L.73, L.75, L.76, F.77, G.79, L.80, F.233 Ligands: PGT.5, J4U.6 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.72, B:L.73, B:F.77, B:F.77, B:L.80, B:F.233, A:L.168, A:L.193 Hydrogen bonds: B:S.69 Salt bridges: B:K.67

2 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.5: 23 residues within 4Å: Chain A: A.154, L.157, S.161, M.165, V.200, R.204, N.205, L.218, P.219, D.220, S.221, R.222, W.224, F.228 Chain B: F.87, E.94, R.226, L.229, V.230, A.232, F.257 Ligands: J4U.6, LHG.11 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.218, A:P.219, A:W.224, A:W.224, A:W.224, A:W.224, B:V.230, B:A.232, B:F.257 Hydrogen bonds: A:R.204, A:N.205, A:S.221, A:S.221, A:R.222, A:R.222 Salt bridges: B:R.226, B:R.226 PGT.12: 23 residues within 4Å: Chain A: F.87, E.94, R.226, L.229, V.230, A.232, F.257 Chain B: A.154, L.157, S.161, M.165, V.200, R.204, N.205, L.218, P.219, D.220, S.221, R.222, W.224, F.228 Ligands: LHG.4, J4U.7 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:V.230, A:A.232, A:F.257, B:L.218, B:P.219, B:W.224, B:W.224, B:W.224, B:W.224 Salt bridges: A:R.226, A:R.226 Hydrogen bonds: B:R.204, B:N.205, B:S.221, B:S.221, B:R.222, B:R.222

2 x J4U: (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol(Non-covalent)

J4U.6: 19 residues within 4Å: Chain A: M.165, L.168, V.169, D.172, P.176, D.181, G.182, W.184, R.186 Chain B: L.73, F.77, A.236, S.240, Y.243, V.244, E.248, W.253 Ligands: PGT.5, LHG.11 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:M.165, A:L.168, A:L.168, A:V.169, B:L.73, B:F.77, B:F.77, B:Y.243, B:V.244, B:W.253, B:W.253 Hydrogen bonds: A:D.172, A:D.172, A:D.181, A:D.181, A:G.182 J4U.7: 19 residues within 4Å: Chain A: L.73, F.77, A.236, S.240, Y.243, V.244, E.248, W.253 Chain B: M.165, L.168, V.169, D.172, P.176, D.181, G.182, W.184, R.186 Ligands: LHG.4, PGT.12 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.73, A:F.77, A:F.77, A:Y.243, A:V.244, A:W.253, A:W.253, B:M.165, B:L.168, B:L.168, B:V.169 Hydrogen bonds: B:D.172, B:D.172, B:D.181, B:D.181, B:G.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, D. et al., Phospholipid translocation captured in a bifunctional membrane protein MprF. Nat Commun (2021)

Release Date

2021-04-21

Peptides

Bifunctional lysylphosphatidylglycerol flippase/synthetase MprF: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Bifunctional lysylphosphatidylglycerol flippase/synthetase MprF

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