SMTL ID : 8d4g.1

gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-6-2-4-2-2-2-mer

Ligands

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

GTP.1: 14 residues within 4Å: Chain B: A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, G.69, A.160, T.161 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.27, B:A.28, B:G.29, B:K.30, B:T.31, B:T.32, B:T.48, B:A.160, B:T.161 GTP.3: 14 residues within 4Å: Chain D: A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, G.69, A.160, T.161 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.27, D:A.28, D:G.29, D:K.30, D:T.31, D:T.32, D:T.48, D:A.160, D:T.161 GTP.5: 14 residues within 4Å: Chain J: A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, G.69, A.160, T.161 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:A.27, J:A.28, J:G.29, J:K.30, J:T.31, J:T.32, J:T.48, J:A.160, J:T.161 GTP.7: 14 residues within 4Å: Chain L: A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, G.69, A.160, T.161 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:A.27, L:A.28, L:G.29, L:K.30, L:T.31, L:T.32, L:T.48, L:A.160, L:T.161 GTP.9: 14 residues within 4Å: Chain N: A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, G.69, A.160, T.161 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:A.27, N:A.28, N:G.29, N:K.30, N:T.31, N:T.32, N:T.48, N:A.160, N:T.161 GTP.11: 14 residues within 4Å: Chain T: A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, G.69, A.160, T.161 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain T Hydrogen bonds: T:A.27, T:A.28, T:G.29, T:K.30, T:T.31, T:T.32, T:T.48, T:A.160, T:T.161

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.48 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain D: T.48 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain J: T.48 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain L: T.48 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain N: T.48 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain T: T.48 Ligands: GTP.11 No protein-ligand interaction detected (PLIP)

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

2023-06-14

Peptides

AP-1 complex subunit beta-1: AK
ADP-ribosylation factor 1: BDJLNT
AP-1 complex subunit gamma-1: CM
Protein Nef: EGOQ
AP-1 complex subunit mu-1: FP
AP-1 complex subunit sigma-3: HR
HLA class I histocompatibility antigen, A alpha chain: IS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

K
A

B
C

D
H

J
Z

L
D

N
F

T
Q

C
G

M
E

E
L

G
N

O
I

Q
K

F
M

P
J

H
S

R
O

I
Y

S
P

AP-1 complex subunit beta-1

ADP-ribosylation factor 1

AP-1 complex subunit gamma-1

Protein Nef

AP-1 complex subunit mu-1

AP-1 complex subunit sigma-3

HLA class I histocompatibility antigen, A alpha chain

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