SMTL ID : 8d9t.1

AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-6-6-6-6-6-mer

Ligands

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

GTP.1: 15 residues within 4Å: Chain A: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.27, A:A.28, A:G.29, A:K.30, A:T.31, A:T.32, A:T.48, A:G.70, A:K.127, A:A.160, A:T.161 GTP.3: 15 residues within 4Å: Chain B: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.4 11 PLIP interactions: 11 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:G.70, B:K.127, B:A.160, B:T.161 GTP.5: 15 residues within 4Å: Chain J: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.6 11 PLIP interactions: 11 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:G.70, J:K.127, J:A.160, J:T.161 GTP.7: 15 residues within 4Å: Chain K: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:A.27, K:A.28, K:G.29, K:K.30, K:T.31, K:T.32, K:T.48, K:G.70, K:K.127, K:A.160, K:T.161 GTP.9: 15 residues within 4Å: Chain S: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain S Hydrogen bonds: S:A.27, S:A.28, S:G.29, S:K.30, S:T.31, S:T.32, S:T.48, S:G.70, S:K.127, S:A.160, S:T.161 GTP.11: 15 residues within 4Å: Chain T: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.12 11 PLIP interactions: 11 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:G.70, T:K.127, T:A.160, T:T.161 GTP.13: 15 residues within 4Å: Chain 1: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain 1 Hydrogen bonds: 1:A.27, 1:A.28, 1:G.29, 1:K.30, 1:T.31, 1:T.32, 1:T.48, 1:G.70, 1:K.127, 1:A.160, 1:T.161 GTP.15: 15 residues within 4Å: Chain 2: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain 2 Hydrogen bonds: 2:A.27, 2:A.28, 2:G.29, 2:K.30, 2:T.31, 2:T.32, 2:T.48, 2:G.70, 2:K.127, 2:A.160, 2:T.161 GTP.17: 15 residues within 4Å: Ligands: MG.18 Chain a: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 11 PLIP interactions: 11 interactions with chain a Hydrogen bonds: a:A.27, a:A.28, a:G.29, a:K.30, a:T.31, a:T.32, a:T.48, a:G.70, a:K.127, a:A.160, a:T.161 GTP.19: 15 residues within 4Å: Ligands: MG.20 Chain b: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 11 PLIP interactions: 11 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:G.70, b:K.127, b:A.160, b:T.161 GTP.21: 15 residues within 4Å: Ligands: MG.22 Chain j: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 11 PLIP interactions: 11 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:G.70, j:K.127, j:A.160, j:T.161 GTP.23: 15 residues within 4Å: Ligands: MG.24 Chain k: D.26, A.27, A.28, G.29, K.30, T.31, T.32, T.45, I.46, P.47, T.48, K.127, A.160, T.161 11 PLIP interactions: 11 interactions with chain k Hydrogen bonds: k:A.27, k:A.28, k:G.29, k:K.30, k:T.31, k:T.32, k:T.48, k:G.70, k:K.127, k:A.160, k:T.161

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.31 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: T.31 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain J: T.31 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain K: T.31 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain S: T.31 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain T: T.31 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain 1: T.31 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain 2: T.31 Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Ligands: GTP.17 Chain a: T.31 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Ligands: GTP.19 Chain b: T.31 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Ligands: GTP.21 Chain j: T.31 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Ligands: GTP.23 Chain k: T.31 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

2022-11-09

Peptides

ADP ribosylation factor 1: ABJKST12abjk
Protein Nef: CGLPUY37cglp
HLA class I histocompatibility antigen, A alpha chain: DMV4dm
AP-1 complex subunit beta-1: ENW5en
AP-1 complex subunit gamma-1: FOX6fo
AP-1 complex subunit mu-1: HQZ8hq
AP-1 complex subunit sigma-3: IR09ir

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

J
J

K
X

S
K

T
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1
O

2
a

a
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b
b

j
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k
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C
N

G
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L
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P
d

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Y
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3
p

7
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c
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g
g

l
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p
h

D
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M
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V
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4
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d
0

m
1

E
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5
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e
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n
I

F
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6
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f
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H
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j

8
k

h
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q
m

I
S

R
s

0
t

9
u

i
v

r
w

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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