SMTL ID : 8d9w.1

beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain E: T.30, T.47 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain K: T.30, T.47 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

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

GTP.2: 16 residues within 4Å: Chain E: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, P.46, T.47, G.68, G.69, K.126, A.159, T.160 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:A.26, E:A.27, E:G.28, E:K.29, E:T.30, E:T.31, E:T.44, E:T.47, E:G.69, E:A.159, E:T.160 GTP.3: 16 residues within 4Å: Chain K: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, P.46, T.47, G.68, G.69, K.126, A.159, T.160 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:A.26, K:A.27, K:G.28, K:K.29, K:T.30, K:T.31, K:T.44, K:T.47, K:G.69, K:A.159, K:T.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hooy, R.M. et al., Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. Sci Adv (2022)

Release Date

2023-07-05

Peptides

Protein Nef: AHNQ
HLA class I histocompatibility antigen, A alpha chain: BR
AP-1 complex subunit beta-1: CFLS
AP-1 complex subunit mu-1: DIOT
ADP-ribosylation factor 1: EK
AP-1 complex subunit gamma-1: GM
AP-1 complex subunit sigma-3: JP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

H
U

N
V

Q
d

B
Y

R
j

C
B

F
A

L
D

S
E

D
M

I
X

O
Z

T
a

E
F

K
I

G
K

M
O

J
e

P
f

Protein Nef

HLA class I histocompatibility antigen, A alpha chain

AP-1 complex subunit beta-1

AP-1 complex subunit mu-1

ADP-ribosylation factor 1

AP-1 complex subunit gamma-1

AP-1 complex subunit sigma-3

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