SMTL ID : 6d84.1

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-4-2-2-2-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain D: D.38, A.39, A.40, G.41, K.42, T.43, T.44, T.57, I.58, P.59, T.60, G.81, G.82, L.83, N.138, K.139, D.141, C.171, A.172 Ligands: MG.2 16 PLIP interactions: 16 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.43, D:T.44, D:T.44, D:T.60, D:T.60, D:G.82, D:A.172 Salt bridges: D:K.42, D:K.42, D:D.141 GTP.3: 19 residues within 4Å: Chain F: A.39, A.40, G.41, K.42, T.43, T.44, T.57, I.58, P.59, T.60, G.82, L.83, N.138, K.139, D.141, C.171, A.172, T.173 Ligands: MG.4 18 PLIP interactions: 18 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.44, F:T.44, F:T.57, F:T.60, F:T.60, F:G.82, F:N.138, F:K.139, F:A.172, F:T.173, F:T.173 Salt bridges: F:D.141 GTP.5: 19 residues within 4Å: Chain L: D.38, A.39, A.40, G.41, K.42, T.43, T.44, T.57, I.58, P.59, T.60, G.81, G.82, L.83, K.139, D.141, C.171, A.172 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:A.39, L:A.40, L:G.41, L:K.42, L:T.43, L:T.43, L:T.43, L:T.44, L:T.44, L:T.60, L:T.60, L:G.82, L:A.172 Salt bridges: L:K.42, L:K.42, L:D.141 GTP.7: 18 residues within 4Å: Chain N: A.39, A.40, G.41, K.42, T.43, T.44, T.57, I.58, P.59, T.60, L.83, N.138, K.139, D.141, C.171, A.172, T.173 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain N Hydrogen bonds: N:A.39, N:A.40, N:G.41, N:K.42, N:T.43, N:T.43, N:T.44, N:T.44, N:T.57, N:T.60, N:N.138, N:K.139, N:A.172, N:T.173, N:T.173 Salt bridges: N:D.141

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain D: T.43, T.60 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 MG.6: 3 residues within 4Å: Chain L: T.43, T.60 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.43, L:T.60 MG.8: 3 residues within 4Å: Chain N: T.43, T.60 Ligands: GTP.7 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:T.43, N: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: ABIJ
AP-1 complex subunit beta-1: CK
ADP-ribosylation factor 1: DFLN
AP-1 complex subunit gamma-1: EM
AP-1 complex subunit mu-1: GO
AP-1 complex subunit sigma-3: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

B
L

I
R

J
O

C
B

K
F

D
C

F
H

L
I

N
N

E
G

M
K

G
M

O
P

H
S

P
Q

Bone marrow stromal antigen 2,Protein Nef

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

Related Entries With Identical Sequence