SMTL ID : 8d4d.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, G.68, G.69, K.126, A.159, T.160 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.26, A:A.27, A:G.28, A:K.29, A:T.30, A:T.31, A:T.44, A:T.47, A:G.69, A:A.159, A:T.160 GTP.3: 17 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, G.68, G.69, K.126, A.159, T.160 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.26, B:A.27, B:G.28, B:K.29, B:T.30, B:T.31, B:T.44, B:T.47, B:G.69, B:A.159, B:T.160 GTP.5: 17 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, G.68, G.69, K.126, A.159, T.160 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:A.26, J:A.27, J:G.28, J:K.29, J:T.30, J:T.31, J:T.44, J:T.47, J:G.69, J:A.159, J:T.160 GTP.7: 17 residues within 4Å: Chain K: D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, I.45, P.46, T.47, G.68, G.69, K.126, A.159, T.160 Ligands: MG.8 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.30 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: T.30 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain J: T.30 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain K: T.30 Ligands: GTP.7 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

ADP-ribosylation factor 1: ABJK
Protein Nef: CGLP
HLA class I histocompatibility antigen, A alpha chain: DM
AP-1 complex subunit beta-1: EN
AP-1 complex subunit gamma-1: FO
AP-1 complex subunit mu-1: HQ
AP-1 complex subunit sigma-3: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

J
D

K
F

C
N

G
L

L
K

P
I

D
Y

M
P

E
B

N
A

F
G

O
E

H
M

Q
J

I
S

R
O

ADP-ribosylation factor 1

Protein Nef

HLA class I histocompatibility antigen, A alpha chain

AP-1 complex subunit beta-1

AP-1 complex subunit gamma-1

AP-1 complex subunit mu-1

AP-1 complex subunit sigma-3

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