SMTL ID : 8s5e.1

Cryo-EM structure of Arf1-decorated membrane tubules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.30, T.31, T.48, D.67 Ligands: GSP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.31, A:T.48, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain B: K.30, T.31, T.48, D.67 Ligands: GSP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.31, B:T.48, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain C: K.30, T.31, T.48, D.67 Ligands: GSP.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.31, C:T.48, H2O.1, H2O.1 MG.7: 5 residues within 4Å: Chain D: K.30, T.31, T.48, D.67 Ligands: GSP.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.31, D:T.48, H2O.1, H2O.1 MG.9: 5 residues within 4Å: Chain E: K.30, T.31, T.48, D.67 Ligands: GSP.10 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.31, E:T.48, H2O.1, H2O.1 MG.11: 5 residues within 4Å: Chain F: K.30, T.31, T.48, D.67 Ligands: GSP.12 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.31, F:T.48, H2O.1, H2O.1 MG.13: 5 residues within 4Å: Chain G: K.30, T.31, T.48, D.67 Ligands: GSP.14 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.31, G:T.48, H2O.1, H2O.1

7 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.2: 21 residues within 4Å: Chain A: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.27, A:A.28, A:G.29, A:K.30, A:T.31, A:T.32, A:T.32, A:T.32, A:T.45, A:T.48, A:T.48, A:T.48, A:G.70, A:N.126, A:K.127, A:K.127, A:A.160 Water bridges: A:T.31, A:T.31, A:T.31, A:I.46 Salt bridges: A:K.30, A:D.129 pi-Cation interactions: A:K.127 GSP.4: 21 residues within 4Å: Chain B: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.27, B:A.28, B:G.29, B:K.30, B:T.31, B:T.32, B:T.32, B:T.32, B:T.45, B:T.48, B:T.48, B:T.48, B:G.70, B:N.126, B:K.127, B:K.127, B:A.160 Water bridges: B:T.31, B:T.31, B:T.31, B:I.46 Salt bridges: B:K.30, B:D.129 pi-Cation interactions: B:K.127 GSP.6: 21 residues within 4Å: Chain C: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.5 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.27, C:A.28, C:G.29, C:K.30, C:T.31, C:T.32, C:T.32, C:T.32, C:T.45, C:T.48, C:T.48, C:T.48, C:G.70, C:N.126, C:K.127, C:K.127, C:A.160 Water bridges: C:T.31, C:T.31, C:T.31, C:I.46 Salt bridges: C:K.30, C:D.129 pi-Cation interactions: C:K.127 GSP.8: 21 residues within 4Å: Chain D: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.7 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:G.27, D:A.28, D:G.29, D:K.30, D:T.31, D:T.32, D:T.32, D:T.32, D:T.45, D:T.48, D:T.48, D:T.48, D:G.70, D:N.126, D:K.127, D:K.127, D:A.160 Water bridges: D:T.31, D:T.31, D:I.46 Salt bridges: D:K.30, D:D.129 pi-Cation interactions: D:K.127 GSP.10: 21 residues within 4Å: Chain E: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.9 23 PLIP interactions: 23 interactions with chain E Hydrogen bonds: E:G.27, E:A.28, E:G.29, E:K.30, E:T.31, E:T.32, E:T.32, E:T.32, E:T.45, E:T.48, E:T.48, E:T.48, E:G.70, E:N.126, E:K.127, E:K.127, E:A.160 Water bridges: E:T.31, E:T.31, E:I.46 Salt bridges: E:K.30, E:D.129 pi-Cation interactions: E:K.127 GSP.12: 21 residues within 4Å: Chain F: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.11 24 PLIP interactions: 24 interactions with chain F Hydrogen bonds: F:G.27, F:A.28, F:G.29, F:K.30, F:T.31, F:T.32, F:T.32, F:T.32, F:T.45, F:T.48, F:T.48, F:T.48, F:G.70, F:N.126, F:K.127, F:K.127, F:A.160 Water bridges: F:T.31, F:T.31, F:T.31, F:I.46 Salt bridges: F:K.30, F:D.129 pi-Cation interactions: F:K.127 GSP.14: 21 residues within 4Å: Chain G: D.26, G.27, A.28, G.29, K.30, T.31, T.32, T.45, P.47, T.48, G.69, G.70, Q.71, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.13 24 PLIP interactions: 24 interactions with chain G Hydrogen bonds: G:G.27, G:A.28, G:G.29, G:K.30, G:T.31, G:T.32, G:T.32, G:T.32, G:T.45, G:T.48, G:T.48, G:T.48, G:G.70, G:N.126, G:K.127, G:K.127, G:A.160 Water bridges: G:T.31, G:T.31, G:T.31, G:I.46 Salt bridges: G:K.30, G:D.129 pi-Cation interactions: G:K.127

Links

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Citation

Haupt, C. et al., Cryo-EM structure of Arf1-decorated membrane tubules. Cell Structure (2024)

Release Date

2025-01-22

Peptides

ADP-ribosylation factor 1: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ADP-ribosylation factor 1

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