SMTL ID : 6cm9.1

Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-2-1-1-1-mer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 17 residues within 4Å: Chain D: D.38, A.39, A.40, G.41, K.42, T.43, T.44, T.57, P.59, T.60, G.81, G.82, K.139, D.141, A.172, T.173 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:A.39, D:A.40, D:G.41, D:K.42, D:T.43, D:T.43, D:T.44, D:T.44, D:T.60, D:T.60, D:T.60, D:G.82, D:A.172, D:T.173 Salt bridges: D:K.42, D:K.42, D:D.141 GTP.3: 17 residues within 4Å: Chain F: A.39, A.40, G.41, K.42, T.43, T.44, T.57, T.60, G.81, G.82, L.83, N.138, K.139, D.141, A.172, T.173 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:A.39, F:A.40, F:G.41, F:K.42, F:T.43, F:T.43, F:T.43, F:T.44, F:T.44, F:T.60, F:T.60, F:G.82, F:A.172, F:T.173 Salt bridges: F:D.141

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain D: T.43, T.60, D.79 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.43, D:T.60 MG.4: 3 residues within 4Å: Chain F: T.43, T.60 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.43, F:T.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morris, K.L. et al., HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Cell (2018)

Release Date

2018-08-08

Peptides

Bone marrow stromal antigen 2, Protein Nef chimera: ABI
AP-1 complex subunit beta-1: C
ADP-ribosylation factor 1: DF
AP-1 complex subunit gamma-1: E
AP-1 complex subunit mu-1: G
AP-1 complex subunit sigma-3: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
T

I
N

C
B

D
C

F
H

E
G

G
M

H
S

Bone marrow stromal antigen 2, Protein Nef chimera

AP-1 complex subunit beta-1

ADP-ribosylation factor 1

AP-1 complex subunit gamma-1

AP-1 complex subunit mu-1

AP-1 complex subunit sigma-3

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