SMTL ID : 6sp2.1

CryoEM structure of SERINC from Drosophila melanogaster

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.1: 12 residues within 4Å: Chain A: N.138, W.140, P.141, F.144, L.145, F.148 Chain B: F.139, L.142, L.145 Ligands: LMN.6, LMN.7, LMN.23 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.144, A:L.145, A:F.148, A:F.148, B:L.142, B:L.145, B:L.145 Hydrogen bonds: A:N.138, A:N.138 LMN.4: 13 residues within 4Å: Chain A: M.68, I.72, I.152, F.156 Chain F: L.52, I.55, G.60, L.61, Q.62, T.64, L.65, M.68 Ligands: LMN.23 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:I.152, A:F.156, A:F.156, F:L.52, F:I.55 Hydrogen bonds: A:I.72, F:G.60, F:T.64, F:L.65 LMN.6: 13 residues within 4Å: Chain A: L.52, I.55, G.60, L.61, Q.62, T.64, L.65, M.68 Chain B: M.68, I.72, I.152, F.156 Ligands: LMN.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.52, A:I.55, B:I.152, B:F.156, B:F.156 Hydrogen bonds: A:G.60, A:T.64, A:L.65 LMN.7: 11 residues within 4Å: Chain B: N.138, W.140, P.141, F.144, L.145, F.148 Chain C: F.139, L.142, L.145 Ligands: LMN.1, LMN.10 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.142, C:L.145, C:L.145, B:F.144, B:L.145, B:F.148, B:F.148 Hydrogen bonds: B:N.138, B:N.138 LMN.10: 13 residues within 4Å: Chain B: L.52, I.55, G.60, L.61, Q.62, T.64, L.65, M.68 Chain C: M.68, I.72, I.152, F.156 Ligands: LMN.7 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.152, C:F.156, C:F.156, B:L.52, B:I.55 Hydrogen bonds: B:G.60, B:T.64, B:L.65 LMN.11: 10 residues within 4Å: Chain C: N.138, W.140, P.141, F.144, L.145, F.148 Chain D: F.139, L.142, L.145 Ligands: LMN.14 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.144, C:L.145, C:F.148, C:F.148, D:L.142, D:L.145, D:L.145 Hydrogen bonds: C:N.138, C:N.138 LMN.14: 13 residues within 4Å: Chain C: L.52, I.55, G.60, L.61, Q.62, T.64, L.65, M.68 Chain D: M.68, I.72, I.152, F.156 Ligands: LMN.11 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.52, C:I.55, D:I.152, D:F.156, D:F.156 Hydrogen bonds: C:G.60, C:T.64, C:L.65, D:I.72 LMN.15: 11 residues within 4Å: Chain D: N.138, W.140, P.141, F.144, L.145, F.148 Chain E: F.139, L.142, L.145 Ligands: LMN.18, LMN.19 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.144, D:L.145, D:F.148, D:F.148, E:L.142, E:L.145, E:L.145 Hydrogen bonds: D:N.138, D:N.138 LMN.18: 13 residues within 4Å: Chain D: L.52, I.55, G.60, L.61, Q.62, T.64, L.65, M.68 Chain E: M.68, I.72, I.152, F.156 Ligands: LMN.15 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:I.152, E:F.156, E:F.156, D:L.52, D:I.55 Hydrogen bonds: E:I.72, D:G.60, D:T.64, D:L.65 LMN.19: 12 residues within 4Å: Chain E: N.138, W.140, P.141, F.144, L.145, F.148 Chain F: F.139, L.142, L.145 Ligands: LMN.15, LMN.22, LMN.23 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:F.144, E:L.145, E:F.148, E:F.148, F:L.142, F:L.145, F:L.145 Hydrogen bonds: E:N.138, E:N.138 LMN.22: 13 residues within 4Å: Chain E: L.52, I.55, G.60, L.61, Q.62, T.64, L.65, M.68 Chain F: M.68, I.72, I.152, F.156 Ligands: LMN.19 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:L.52, E:I.55, F:I.152, F:F.156, F:F.156 Hydrogen bonds: E:G.60, E:T.64, E:L.65, F:I.72 LMN.23: 12 residues within 4Å: Chain A: F.139, L.142, L.145 Chain F: N.138, W.140, P.141, F.144, L.145, F.148 Ligands: LMN.1, LMN.4, LMN.19 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:F.144, F:L.145, F:F.148, F:F.148, A:L.142, A:L.145, A:L.145 Hydrogen bonds: F:N.138, F:N.138

6 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.2: 10 residues within 4Å: Chain A: G.224, L.228, Y.231, F.232, L.281, Y.285, W.288, G.302, I.334 Ligands: CDL.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.228, A:L.281, A:Y.285, A:W.288, A:W.288, A:I.334 P5S.8: 10 residues within 4Å: Chain B: G.224, L.228, Y.231, F.232, L.281, Y.285, W.288, G.302, I.334 Ligands: CDL.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.228, B:L.281, B:Y.285, B:W.288, B:W.288, B:I.334 P5S.12: 10 residues within 4Å: Chain C: G.224, L.228, Y.231, F.232, L.281, Y.285, W.288, G.302, I.334 Ligands: CDL.13 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.228, C:L.281, C:Y.285, C:W.288, C:W.288, C:I.334 P5S.16: 10 residues within 4Å: Chain D: G.224, L.228, Y.231, F.232, L.281, Y.285, W.288, G.302, I.334 Ligands: CDL.17 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.228, D:L.281, D:Y.285, D:W.288, D:W.288, D:I.334 P5S.20: 10 residues within 4Å: Chain E: G.224, L.228, Y.231, F.232, L.281, Y.285, W.288, G.302, I.334 Ligands: CDL.21 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.228, E:L.281, E:Y.285, E:W.288, E:W.288, E:I.334 P5S.24: 10 residues within 4Å: Chain F: G.224, L.228, Y.231, F.232, L.281, Y.285, W.288, G.302, I.334 Ligands: CDL.3 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.228, F:L.281, F:Y.285, F:W.288, F:W.288, F:I.334

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 17 residues within 4Å: Chain A: F.109, I.146, A.150, G.153, A.154, I.157, P.158, S.161, A.165 Chain F: L.47, V.51, A.54, F.328, T.330, L.336, V.337 Ligands: P5S.24 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: A:F.109, A:I.146, A:A.150, A:I.157, A:A.165, F:L.47, F:L.47, F:V.51, F:F.328, F:L.336, F:V.337 Hydrogen bonds: A:S.161, A:S.161 CDL.5: 18 residues within 4Å: Chain A: L.47, V.51, A.54, F.328, T.330, L.336, V.337 Chain B: F.109, I.146, A.150, G.153, A.154, I.157, P.158, D.159, S.161, A.165 Ligands: P5S.2 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.47, A:L.47, A:V.51, A:F.328, A:L.336, A:V.337, B:F.109, B:I.146, B:A.150, B:I.157, B:A.165 Hydrogen bonds: B:S.161, B:S.161 CDL.9: 17 residues within 4Å: Chain B: L.47, V.51, A.54, F.328, T.330, L.336, V.337 Chain C: F.109, I.146, A.150, G.153, A.154, I.157, P.158, S.161, A.165 Ligands: P5S.8 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:F.109, C:I.146, C:A.150, C:I.157, C:A.165, B:L.47, B:L.47, B:V.51, B:F.328, B:L.336, B:V.337 Hydrogen bonds: C:S.161, C:S.161 CDL.13: 17 residues within 4Å: Chain C: L.47, V.51, A.54, F.328, T.330, L.336, V.337 Chain D: F.109, I.146, A.150, G.153, A.154, I.157, P.158, S.161, A.165 Ligands: P5S.12 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.109, D:I.146, D:A.150, D:I.157, D:A.165, C:L.47, C:L.47, C:V.51, C:F.328, C:L.336, C:V.337 Hydrogen bonds: D:S.161, D:S.161 CDL.17: 17 residues within 4Å: Chain D: L.47, V.51, A.54, F.328, T.330, L.336, V.337 Chain E: F.109, I.146, A.150, G.153, A.154, I.157, P.158, S.161, A.165 Ligands: P5S.16 13 PLIP interactions: 7 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:F.109, E:I.146, E:A.150, E:I.157, E:A.165, D:L.47, D:L.47, D:V.51, D:F.328, D:L.336, D:V.337 Hydrogen bonds: E:S.161, E:S.161 CDL.21: 17 residues within 4Å: Chain E: L.47, V.51, A.54, F.328, T.330, L.336, V.337 Chain F: F.109, I.146, A.150, G.153, A.154, I.157, P.158, S.161, A.165 Ligands: P5S.20 13 PLIP interactions: 7 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:F.109, F:I.146, F:A.150, F:I.157, F:A.165, E:L.47, E:L.47, E:V.51, E:F.328, E:L.336, E:V.337 Hydrogen bonds: F:S.161, F:S.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pye, V.E. et al., A bipartite structural organization defines the SERINC family of HIV-1 restriction factors. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-01-01

Peptides

Membrane protein TMS1d: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Membrane protein TMS1d