SMTL ID : 7ojf.1

CRYO-EM STRUCTURE OF SLYB13-BAMA FROM ESCHERICHIA COLI

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-13-1-mer

Ligands

13 x PLM: PALMITIC ACID(Covalent)

PLM.1: 9 residues within 4Å: Chain A: C.18, I.62, G.63, G.66, G.67, V.102, M.106 Chain M: V.97, Q.100 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain A Hydrophobic interactions: M:V.97, A:I.62, A:V.102 PLM.5: 5 residues within 4Å: Chain A: V.97 Chain B: C.18, G.67, V.102, M.106 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.97, B:V.102 PLM.8: 9 residues within 4Å: Chain B: V.97 Chain C: C.18, G.63, G.66, G.67, G.95, V.102, Q.103, M.106 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.102, B:V.97 PLM.12: 8 residues within 4Å: Chain C: V.97 Chain D: C.18, V.19, G.63, G.67, L.70, Q.103, M.106 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.70, D:Q.103 PLM.17: 9 residues within 4Å: Chain D: V.97, Q.100 Chain E: C.18, I.62, G.63, A.98, V.102, Q.103, M.106 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.62, E:A.98, D:V.97 PLM.20: 6 residues within 4Å: Chain E: V.97 Chain F: C.18, G.63, G.67, V.102, M.106 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:V.102, E:V.97 PLM.24: 9 residues within 4Å: Chain F: Q.100 Chain G: C.18, I.62, G.63, A.94, G.95, A.98, V.102, M.106 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.94, G:A.98, G:V.102 PLM.27: 6 residues within 4Å: Chain G: V.97 Chain H: C.18, G.67, L.70, G.95, V.102 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:L.70, H:V.102, G:V.97 PLM.32: 8 residues within 4Å: Chain H: V.97, Q.100 Chain I: C.18, G.63, G.67, V.102, Q.103, M.106 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:V.102, I:Q.103, H:V.97 PLM.35: 9 residues within 4Å: Chain I: V.97, Q.100 Chain J: C.18, G.63, G.66, G.67, V.102, Q.103, M.106 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:V.102, J:Q.103, I:V.97 PLM.40: 8 residues within 4Å: Chain J: V.97, Q.100 Chain K: C.18, G.63, G.67, V.102, Q.103, M.106 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: K:V.102, K:Q.103, J:V.97 PLM.44: 6 residues within 4Å: Chain K: Q.100 Chain L: C.18, I.62, G.63, G.67, M.106 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:I.62 PLM.48: 6 residues within 4Å: Chain L: V.97, Q.100 Chain M: C.18, G.63, V.102, Q.103 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: M:V.102, M:Q.103, L:V.97

13 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.2: 13 residues within 4Å: Chain A: T.77, V.78, G.79, G.80, G.81, T.82, G.83, R.84, L.86, A.90 Chain B: T.77 Ligands: L8Z.6, L8Z.50 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.77, A:L.86, A:L.86, A:A.90, B:T.77 Hydrogen bonds: A:G.79, A:G.80, A:T.82, A:T.82, A:G.83 L8Z.6: 13 residues within 4Å: Chain B: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90 Chain C: T.77 Ligands: L8Z.2, L8Z.10 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.77, B:A.87, B:A.90, C:T.77 Hydrogen bonds: B:G.79, B:G.80, B:T.82, B:T.82 L8Z.10: 10 residues within 4Å: Chain C: L.74, V.78, G.79, G.80, T.82, G.83, L.86 Chain D: T.77 Ligands: L8Z.6, L8Z.14 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.74, C:L.86 Hydrogen bonds: C:G.79, C:G.80, C:T.82, C:T.82, C:T.82 L8Z.14: 13 residues within 4Å: Chain D: T.77, V.78, G.79, G.80, T.82, G.83, L.86, A.87, A.90 Chain E: L.74, T.77 Ligands: L8Z.10, L8Z.18 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:T.77, D:L.86, D:A.87, E:L.74 Hydrogen bonds: D:G.79, D:G.80, D:T.82, D:T.82 L8Z.18: 12 residues within 4Å: Chain E: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87 Chain F: T.77 Ligands: L8Z.14, L8Z.21 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:T.77, E:A.87, F:T.77 Hydrogen bonds: E:G.79, E:G.80, E:T.82, E:T.82 L8Z.21: 14 residues within 4Å: Chain F: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90 Chain G: L.70, T.77 Ligands: L8Z.18, L8Z.25 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:T.77, F:V.78, F:L.86, F:A.87, G:L.70 Hydrogen bonds: F:G.79, F:G.80, F:T.82, F:T.82 L8Z.25: 12 residues within 4Å: Chain G: T.77, V.78, G.79, G.80, T.82, G.83, L.86, A.87, A.90 Chain H: T.77 Ligands: L8Z.21, L8Z.29 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:V.78, G:A.87, H:T.77 Hydrogen bonds: G:G.79, G:G.80, G:T.82, G:G.83 L8Z.29: 13 residues within 4Å: Chain H: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90 Chain I: T.77 Ligands: L8Z.25, L8Z.33 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:V.78, H:L.86, H:A.87, H:A.90 Hydrogen bonds: H:G.79, H:G.80, H:T.82, H:T.82, H:T.82 L8Z.33: 13 residues within 4Å: Chain I: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90 Chain J: T.77 Ligands: L8Z.29, L8Z.37 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:V.78, I:L.86, I:A.87, I:A.90 Hydrogen bonds: I:G.79, I:G.80, I:T.82, I:T.82, I:T.82 L8Z.37: 13 residues within 4Å: Chain J: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90, G.91 Chain K: T.77 Ligands: L8Z.33 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:T.77, J:V.78, J:V.78, J:L.86, J:A.87, J:A.90 Hydrogen bonds: J:G.79, J:G.80, J:T.82, J:T.82 L8Z.41: 12 residues within 4Å: Chain K: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90 Chain L: T.77 Ligands: L8Z.45 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:L.86, K:A.87, L:T.77 Hydrogen bonds: K:G.79, K:G.80, K:T.82 L8Z.45: 13 residues within 4Å: Chain L: T.77, V.78, G.79, G.80, G.81, T.82, G.83, L.86, A.87, A.90 Chain M: T.77 Ligands: L8Z.41, L8Z.50 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:T.77, L:V.78, L:L.86, L:A.90, M:T.77 Hydrogen bonds: L:G.79, L:G.80, L:T.82, L:T.82, L:T.82 L8Z.50: 14 residues within 4Å: Chain A: L.70, T.77 Chain M: T.77, V.78, G.79, G.80, T.82, G.83, R.84, L.86, A.87, A.90 Ligands: L8Z.2, L8Z.45 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain M Hydrophobic interactions: A:L.70, A:T.77, M:T.77, M:V.78, M:L.86, M:A.87, M:A.90 Hydrogen bonds: M:G.79, M:G.80, M:T.82, M:T.82

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

LPP.3: 9 residues within 4Å: Chain A: I.65, A.68, F.73, N.76, T.88, A.89, V.93 Chain B: F.73 Chain N: F.718 8 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B, 1 interactions with chain N Hydrophobic interactions: A:I.65, A:A.68, A:F.73, A:A.89, A:V.93, B:F.73, N:F.718 Hydrogen bonds: A:N.76 LPP.7: 6 residues within 4Å: Chain B: A.68, V.69, G.72, F.73, N.76, T.88 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.68, B:V.69, B:F.73, B:T.88 Hydrogen bonds: B:N.76 LPP.11: 6 residues within 4Å: Chain C: I.65, G.72, F.73, N.76, R.84, V.93 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.65, C:F.73, C:V.93 Hydrogen bonds: C:N.76 Salt bridges: C:R.84 LPP.15: 9 residues within 4Å: Chain D: I.65, A.68, F.73, N.76, T.88, A.89, A.92, V.93 Chain E: F.73 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.65, D:A.68, D:T.88, D:A.89, D:A.92, D:V.93, E:F.73 Hydrogen bonds: D:N.76 LPP.22: 8 residues within 4Å: Chain F: I.65, A.68, V.69, N.76, R.84 Chain N: Y.531, D.568, G.603 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.65, F:A.68, F:V.69 Hydrogen bonds: F:N.76 Salt bridges: F:R.84, F:R.84 LPP.26: 8 residues within 4Å: Chain G: A.68, V.69, G.72, F.73, N.76, R.84, T.88 Chain N: Y.509 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:A.68, G:V.69 Hydrogen bonds: G:N.76 Salt bridges: G:R.84 LPP.30: 6 residues within 4Å: Chain H: I.65, V.69, F.73, N.76, R.84, T.88 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:I.65, H:V.69, H:F.73 Hydrogen bonds: H:N.76 Salt bridges: H:R.84 LPP.34: 7 residues within 4Å: Chain I: I.65, V.69, G.72, F.73, N.76, R.84, T.88 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:I.65, I:V.69, I:F.73, I:T.88 Hydrogen bonds: I:N.76 Salt bridges: I:R.84 LPP.38: 4 residues within 4Å: Chain J: V.69, F.73, N.76, T.88 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:V.69, J:F.73 Hydrogen bonds: J:N.76 LPP.42: 9 residues within 4Å: Chain K: I.65, V.69, F.73, N.76, R.84, T.88, A.92, V.93 Chain L: F.73 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:I.65, K:V.69, K:F.73, K:A.92, L:F.73 Hydrogen bonds: K:N.76 LPP.46: 7 residues within 4Å: Chain L: I.65, V.69, G.72, F.73, N.76, T.88, A.92 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:I.65, L:V.69, L:F.73, L:A.92 Hydrogen bonds: L:N.76 Salt bridges: L:R.84 LPP.51: 5 residues within 4Å: Chain M: I.65, V.69, F.73, N.76, T.88 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:I.65, M:V.69, M:F.73, M:T.88 Hydrogen bonds: M:N.76

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: G.101 No protein-ligand interaction detected (PLIP) GOL.9: 1 residues within 4Å: Chain C: C.18 No protein-ligand interaction detected (PLIP) GOL.13: 1 residues within 4Å: Chain D: C.18 No protein-ligand interaction detected (PLIP) GOL.16: 2 residues within 4Å: Chain D: V.97 Chain E: C.18 No protein-ligand interaction detected (PLIP) GOL.19: 3 residues within 4Å: Chain E: V.97, G.101 Chain F: M.106 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.101 GOL.23: 1 residues within 4Å: Chain F: G.101 No protein-ligand interaction detected (PLIP) GOL.28: 2 residues within 4Å: Chain G: V.97 Chain H: C.18 No protein-ligand interaction detected (PLIP) GOL.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.36: 2 residues within 4Å: Chain J: C.18, M.106 No protein-ligand interaction detected (PLIP) GOL.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.47: 1 residues within 4Å: Chain M: G.101 No protein-ligand interaction detected (PLIP) GOL.49: 2 residues within 4Å: Chain M: C.18, M.106 No protein-ligand interaction detected (PLIP)

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

2022-07-27

Peptides

Outer membrane lipoprotein slyB: ABCDEFGHIJKLM
Outer membrane protein assembly factor BamA: N

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

L
L

M
M

N
N

Membrane

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

Outer membrane protein assembly factor BamA

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