SMTL ID : 8d9r.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-18-12-6-6-6-6-6-mer

Ligands

18 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, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.27, A:G.29, A:K.30, A:T.31, A:T.32, A:I.46, A:T.48, A:G.70, A:K.127, 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, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.27, B:G.29, B:K.30, B:T.31, B:T.32, B:I.46, B:T.48, B:G.70, B:K.127, 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, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:A.27, J:G.29, J:K.30, J:T.31, J:T.32, J:I.46, J:T.48, J:G.70, J:K.127, 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, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:A.27, K:G.29, K:K.30, K:T.31, K:T.32, K:I.46, K:T.48, K:G.70, K:K.127, K:T.161 GTP.9: 15 residues within 4Å: Chain L: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:A.27, L:G.29, L:K.30, L:T.31, L:T.32, L:I.46, L:T.48, L:G.70, L:K.127, L:T.161 GTP.11: 15 residues within 4Å: Chain T: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain T Hydrogen bonds: T:A.27, T:G.29, T:K.30, T:T.31, T:T.32, T:I.46, T:T.48, T:G.70, T:K.127, T:T.161 GTP.13: 15 residues within 4Å: Chain U: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.14 10 PLIP interactions: 10 interactions with chain U Hydrogen bonds: U:A.27, U:G.29, U:K.30, U:T.31, U:T.32, U:I.46, U:T.48, U:G.70, U:K.127, U:T.161 GTP.15: 15 residues within 4Å: Chain V: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.16 10 PLIP interactions: 10 interactions with chain V Hydrogen bonds: V:A.27, V:G.29, V:K.30, V:T.31, V:T.32, V:I.46, V:T.48, V:G.70, V:K.127, V:T.161 GTP.17: 15 residues within 4Å: Chain 3: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.18 10 PLIP interactions: 10 interactions with chain 3 Hydrogen bonds: 3:A.27, 3:G.29, 3:K.30, 3:T.31, 3:T.32, 3:I.46, 3:T.48, 3:G.70, 3:K.127, 3:T.161 GTP.19: 15 residues within 4Å: Chain 4: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain 4 Hydrogen bonds: 4:A.27, 4:G.29, 4:K.30, 4:T.31, 4:T.32, 4:I.46, 4:T.48, 4:G.70, 4:K.127, 4:T.161 GTP.21: 15 residues within 4Å: Chain 5: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 Ligands: MG.22 11 PLIP interactions: 11 interactions with chain 5 Hydrogen bonds: 5:A.27, 5:A.28, 5:G.29, 5:K.30, 5:T.31, 5:T.32, 5:I.46, 5:T.48, 5:G.70, 5:K.127, 5:T.161 GTP.23: 15 residues within 4Å: Ligands: MG.24 Chain d: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 11 PLIP interactions: 11 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:I.46, d:T.48, d:G.70, d:K.127, d:T.161 GTP.25: 15 residues within 4Å: Ligands: MG.26 Chain e: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 10 PLIP interactions: 10 interactions with chain e Hydrogen bonds: e:A.27, e:G.29, e:K.30, e:T.31, e:T.32, e:I.46, e:T.48, e:G.70, e:K.127, e:T.161 GTP.27: 15 residues within 4Å: Ligands: MG.28 Chain f: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 10 PLIP interactions: 10 interactions with chain f Hydrogen bonds: f:A.27, f:G.29, f:K.30, f:T.31, f:T.32, f:I.46, f:T.48, f:G.70, f:K.127, f:T.161 GTP.29: 15 residues within 4Å: Ligands: MG.30 Chain n: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 10 PLIP interactions: 10 interactions with chain n Hydrogen bonds: n:A.27, n:G.29, n:K.30, n:T.31, n:T.32, n:I.46, n:T.48, n:G.70, n:K.127, n:T.161 GTP.31: 15 residues within 4Å: Ligands: MG.32 Chain o: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 11 PLIP interactions: 11 interactions with chain o Hydrogen bonds: o:A.27, o:A.28, o:G.29, o:K.30, o:T.31, o:T.32, o:I.46, o:T.48, o:G.70, o:K.127, o:T.161 GTP.33: 15 residues within 4Å: Ligands: MG.34 Chain p: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 11 PLIP interactions: 11 interactions with chain p Hydrogen bonds: p:A.27, p:A.28, p:G.29, p:K.30, p:T.31, p:T.32, p:I.46, p:T.48, p:G.70, p:K.127, p:T.161 GTP.35: 15 residues within 4Å: Ligands: MG.36 Chain x: D.26, A.27, A.28, G.29, K.30, T.31, T.32, I.46, P.47, T.48, G.69, G.70, K.127, T.161 10 PLIP interactions: 10 interactions with chain x Hydrogen bonds: x:A.27, x:G.29, x:K.30, x:T.31, x:T.32, x:I.46, x:T.48, x:G.70, x:K.127, x:T.161

18 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 L: 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 U: T.31 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain V: T.31 Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain 3: T.31 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain 4: T.31 Ligands: GTP.19 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain 5: T.31 Ligands: GTP.21 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Ligands: GTP.23 Chain d: T.31 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Ligands: GTP.25 Chain e: T.31 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Ligands: GTP.27 Chain f: T.31 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Ligands: GTP.29 Chain n: T.31 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Ligands: GTP.31 Chain o: T.31 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Ligands: GTP.33 Chain p: T.31 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Ligands: GTP.35 Chain x: 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: ABJKLTUV345defnopx
Protein Nef: CGMQW06agkqu
HLA class I histocompatibility antigen, A alpha chain: DNX7hr
AP-1 complex subunit beta-1: EOY8is
AP-1 complex subunit gamma-1: FPZ9jt
AP-1 complex subunit mu-1: HR1blv
AP-1 complex subunit sigma-3: IS2cmw

SMTL:PDB

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PDB Chain Id:

A
C

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H

J
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3

U
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3
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4
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6

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7

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0
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6
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g
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7
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1

r
2

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8
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i
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9
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1
k

b
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l
m

v
n

I
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S
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2
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w
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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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