SMTL ID : 7ojg.1

CRYO-EM STRUCTURE OF UNDECAMERIC SLYB FROM ESCHERICHIA COLI K12

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

homo-11-mer

Ligands

33 x PLM: PALMITIC ACID(Covalent)(Non-covalent)(Non-functional Binders)

PLM.1: 6 residues within 4Å: Chain A: C.18, I.62, G.95, Q.103, M.106 Chain K: Q.100 Ligand excluded by PLIP PLM.5: 4 residues within 4Å: Chain K: V.93, A.94 Ligands: GOL.2, PLM.6 Ligand excluded by PLIP PLM.6: 4 residues within 4Å: Chain K: V.97, G.101 Ligands: GOL.2, PLM.5 Ligand excluded by PLIP PLM.7: 4 residues within 4Å: Chain A: V.97, G.101 Ligands: GOL.9, PLM.10 Ligand excluded by PLIP PLM.8: 6 residues within 4Å: Chain A: Q.100 Chain B: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.10: 3 residues within 4Å: Chain A: A.94 Ligands: PLM.7, GOL.9 Ligand excluded by PLIP PLM.13: 4 residues within 4Å: Chain B: V.97, G.101 Ligands: GOL.15, PLM.16 Ligand excluded by PLIP PLM.14: 6 residues within 4Å: Chain B: Q.100 Chain C: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.16: 3 residues within 4Å: Chain B: A.94 Ligands: PLM.13, GOL.15 Ligand excluded by PLIP PLM.19: 4 residues within 4Å: Chain C: V.97, G.101 Ligands: GOL.21, PLM.22 Ligand excluded by PLIP PLM.20: 6 residues within 4Å: Chain C: Q.100 Chain D: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.22: 3 residues within 4Å: Chain C: A.94 Ligands: PLM.19, GOL.21 Ligand excluded by PLIP PLM.25: 4 residues within 4Å: Chain D: V.97, G.101 Ligands: GOL.27, PLM.28 Ligand excluded by PLIP PLM.26: 6 residues within 4Å: Chain D: Q.100 Chain E: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.28: 3 residues within 4Å: Chain D: A.94 Ligands: PLM.25, GOL.27 Ligand excluded by PLIP PLM.31: 4 residues within 4Å: Chain E: V.97, G.101 Ligands: GOL.33, PLM.34 Ligand excluded by PLIP PLM.32: 6 residues within 4Å: Chain E: Q.100 Chain F: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.34: 3 residues within 4Å: Chain E: A.94 Ligands: PLM.31, GOL.33 Ligand excluded by PLIP PLM.37: 4 residues within 4Å: Chain F: V.97, G.101 Ligands: GOL.39, PLM.40 Ligand excluded by PLIP PLM.38: 6 residues within 4Å: Chain F: Q.100 Chain G: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.40: 3 residues within 4Å: Chain F: A.94 Ligands: PLM.37, GOL.39 Ligand excluded by PLIP PLM.43: 4 residues within 4Å: Chain G: V.97, G.101 Ligands: GOL.45, PLM.46 Ligand excluded by PLIP PLM.44: 6 residues within 4Å: Chain G: Q.100 Chain H: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.46: 3 residues within 4Å: Chain G: A.94 Ligands: PLM.43, GOL.45 Ligand excluded by PLIP PLM.49: 4 residues within 4Å: Chain H: V.97, G.101 Ligands: GOL.51, PLM.52 Ligand excluded by PLIP PLM.50: 6 residues within 4Å: Chain H: Q.100 Chain I: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.52: 3 residues within 4Å: Chain H: A.94 Ligands: PLM.49, GOL.51 Ligand excluded by PLIP PLM.55: 4 residues within 4Å: Chain I: V.97, G.101 Ligands: GOL.57, PLM.58 Ligand excluded by PLIP PLM.56: 6 residues within 4Å: Chain I: Q.100 Chain J: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.58: 3 residues within 4Å: Chain I: A.94 Ligands: PLM.55, GOL.57 Ligand excluded by PLIP PLM.61: 2 residues within 4Å: Ligands: GOL.63, PLM.64 Ligand excluded by PLIP PLM.62: 6 residues within 4Å: Chain J: Q.100 Chain K: C.18, I.62, G.95, Q.103, M.106 Ligand excluded by PLIP PLM.64: 2 residues within 4Å: Ligands: PLM.61, GOL.63 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: C.18 Ligands: PLM.5, PLM.6 No protein-ligand interaction detected (PLIP) GOL.9: 3 residues within 4Å: Chain B: C.18 Ligands: PLM.7, PLM.10 No protein-ligand interaction detected (PLIP) GOL.15: 3 residues within 4Å: Chain C: C.18 Ligands: PLM.13, PLM.16 No protein-ligand interaction detected (PLIP) GOL.21: 3 residues within 4Å: Chain D: C.18 Ligands: PLM.19, PLM.22 No protein-ligand interaction detected (PLIP) GOL.27: 3 residues within 4Å: Chain E: C.18 Ligands: PLM.25, PLM.28 No protein-ligand interaction detected (PLIP) GOL.33: 3 residues within 4Å: Chain F: C.18 Ligands: PLM.31, PLM.34 No protein-ligand interaction detected (PLIP) GOL.39: 3 residues within 4Å: Chain G: C.18 Ligands: PLM.37, PLM.40 No protein-ligand interaction detected (PLIP) GOL.45: 3 residues within 4Å: Chain H: C.18 Ligands: PLM.43, PLM.46 No protein-ligand interaction detected (PLIP) GOL.51: 3 residues within 4Å: Chain I: C.18 Ligands: PLM.49, PLM.52 No protein-ligand interaction detected (PLIP) GOL.57: 3 residues within 4Å: Chain J: C.18 Ligands: PLM.55, PLM.58 No protein-ligand interaction detected (PLIP) GOL.63: 3 residues within 4Å: Chain K: C.18 Ligands: PLM.61, PLM.64 No protein-ligand interaction detected (PLIP)

11 x L8Z: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)

L8Z.3: 11 residues within 4Å: Chain A: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain B: L.70, L.74 Ligands: L8Z.65 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.86, A:A.90, B:L.70, B:L.74 Hydrogen bonds: A:G.79, A:G.80, A:T.82, A:T.82 L8Z.11: 10 residues within 4Å: Chain B: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain C: L.70, L.74 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.86, B:A.90, C:L.70, C:L.74 Hydrogen bonds: B:G.79, B:G.80, B:T.82, B:T.82 L8Z.17: 10 residues within 4Å: Chain C: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain D: L.70, L.74 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:L.70, D:L.74, C:L.86, C:A.90 Hydrogen bonds: C:G.79, C:G.80, C:T.82, C:T.82 L8Z.23: 10 residues within 4Å: Chain D: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain E: L.70, L.74 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:L.86, D:A.90, E:L.70, E:L.74 Hydrogen bonds: D:G.79, D:G.80, D:T.82, D:T.82 L8Z.29: 10 residues within 4Å: Chain E: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain F: L.70, L.74 8 PLIP interactions: 2 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:L.70, F:L.74, E:L.86, E:A.90 Hydrogen bonds: E:G.79, E:G.80, E:T.82, E:T.82 L8Z.35: 10 residues within 4Å: Chain F: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain G: L.70, L.74 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:L.86, F:A.90, G:L.70, G:L.74 Hydrogen bonds: F:G.79, F:G.80, F:T.82, F:T.82 L8Z.41: 10 residues within 4Å: Chain G: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain H: L.70, L.74 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:L.86, G:A.90, H:L.70, H:L.74 Hydrogen bonds: G:G.79, G:G.80, G:T.82, G:T.82 L8Z.47: 10 residues within 4Å: Chain H: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain I: L.70, L.74 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:L.86, H:A.90, I:L.70, I:L.74 Hydrogen bonds: H:G.79, H:G.80, H:T.82, H:T.82 L8Z.53: 10 residues within 4Å: Chain I: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain J: L.70, L.74 8 PLIP interactions: 2 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:L.70, J:L.74, I:L.86, I:A.90 Hydrogen bonds: I:G.79, I:G.80, I:T.82, I:T.82 L8Z.59: 10 residues within 4Å: Chain J: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Chain K: L.70, T.77 8 PLIP interactions: 2 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:L.70, K:T.77, J:L.86, J:A.90 Hydrogen bonds: J:G.79, J:G.80, J:T.82, J:T.82 L8Z.65: 9 residues within 4Å: Chain K: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90 Ligands: L8Z.3 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:L.86, K:A.90 Hydrogen bonds: K:G.79, K:G.80, K:T.82, K:T.82

11 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)

LPP.4: 6 residues within 4Å: Chain A: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.92 Hydrogen bonds: A:N.76 Salt bridges: A:R.84 LPP.12: 6 residues within 4Å: Chain B: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.92 Hydrogen bonds: B:N.76 Salt bridges: B:R.84 LPP.18: 6 residues within 4Å: Chain C: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.92 Hydrogen bonds: C:N.76 Salt bridges: C:R.84 LPP.24: 6 residues within 4Å: Chain D: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.92 Hydrogen bonds: D:N.76 Salt bridges: D:R.84 LPP.30: 6 residues within 4Å: Chain E: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.92 Hydrogen bonds: E:N.76 Salt bridges: E:R.84 LPP.36: 6 residues within 4Å: Chain F: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.92 Hydrogen bonds: F:N.76 Salt bridges: F:R.84 LPP.42: 6 residues within 4Å: Chain G: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.92 Hydrogen bonds: G:N.76 Salt bridges: G:R.84 LPP.48: 6 residues within 4Å: Chain H: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:A.92 Hydrogen bonds: H:N.76 Salt bridges: H:R.84 LPP.54: 6 residues within 4Å: Chain I: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:A.92 Hydrogen bonds: I:N.76 Salt bridges: I:R.84 LPP.60: 6 residues within 4Å: Chain J: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:A.92 Hydrogen bonds: J:N.76 Salt bridges: J:R.84 LPP.66: 6 residues within 4Å: Chain K: A.68, N.76, R.84, S.85, T.88, A.92 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:A.92 Hydrogen bonds: K:N.76 Salt bridges: K:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssens, A. et al., SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains. Nature (2023)

Release Date

2022-08-03

Peptides

Outer membrane lipoprotein slyB: ABCDEFGHIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

Membrane

We predict this structure to be a membrane protein.
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Outer membrane lipoprotein slyB

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