SMTL ID : 8d4f.1

beta-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: 15 residues within 4Å: Chain B: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, K.126, A.159, T.160 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.26, B:A.26, B:G.28, B:K.29, B:T.30, B:T.31, B:T.44, B:T.47, B:K.126, B:A.159, B:T.160 GTP.3: 15 residues within 4Å: Chain D: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, K.126, A.159, T.160 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:A.26, D:A.26, D:G.28, D:K.29, D:T.30, D:T.31, D:T.44, D:T.47, D:K.126, D:A.159, D:T.160 GTP.5: 15 residues within 4Å: Chain J: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, K.126, A.159, T.160 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:A.26, J:A.26, J:G.28, J:K.29, J:T.30, J:T.31, J:T.44, J:T.47, J:K.126, J:A.159, J:T.160 GTP.7: 15 residues within 4Å: Chain L: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, K.126, A.159, T.160 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:A.26, L:A.26, L:G.28, L:K.29, L:T.30, L:T.31, L:T.44, L:T.47, L:K.126, L:A.159, L:T.160 GTP.9: 15 residues within 4Å: Chain N: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, K.126, A.159, T.160 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:A.26, N:A.26, N:G.28, N:K.29, N:T.30, N:T.31, N:T.44, N:T.47, N:K.126, N:A.159, N:T.160 GTP.11: 15 residues within 4Å: Chain T: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, K.126, A.159, T.160 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain T Hydrogen bonds: T:A.26, T:A.26, T:G.28, T:K.29, T:T.30, T:T.31, T:T.44, T:T.47, T:K.126, T:A.159, T:T.160

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: K.29, T.30 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain D: K.29, T.30 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain J: K.29, T.30 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain L: K.29, T.30 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain N: K.29, T.30 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain T: K.29, T.30 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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