SMTL ID : 7dde.1

Cryo-EM structure of the Ape4 and Nbr1 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

48 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.262, E.298, E.299, H.437 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.262, A:E.299, A:H.437 ZN.2: 7 residues within 4Å: Chain A: H.93, D.262, N.263, E.298, E.299, D.343 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, A:D.262, A:D.262, H2O.2 ZN.3: 5 residues within 4Å: Chain A: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.510, A:H.530, A:C.532 ZN.4: 5 residues within 4Å: Chain A: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.496, A:T.498, A:C.499, A:C.519, A:C.522 ZN.5: 5 residues within 4Å: Chain B: D.262, E.298, E.299, H.437 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.262, B:E.299, B:H.437, H2O.4 ZN.6: 6 residues within 4Å: Chain B: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.93, B:D.262, B:D.262 ZN.7: 5 residues within 4Å: Chain B: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.510, B:H.530, B:C.532 ZN.8: 5 residues within 4Å: Chain B: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.496, B:T.498, B:C.499, B:C.519, B:C.522 ZN.9: 5 residues within 4Å: Chain C: D.262, E.298, E.299, H.437 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.262, C:E.299, C:H.437, H2O.71 ZN.10: 6 residues within 4Å: Chain C: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.93, C:D.262, C:D.262 ZN.11: 5 residues within 4Å: Chain C: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.510, C:H.530, C:C.532 ZN.12: 5 residues within 4Å: Chain C: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.496, C:T.498, C:C.499, C:C.519, C:C.522 ZN.13: 5 residues within 4Å: Chain D: D.262, E.298, E.299, H.437 Ligands: ZN.14 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.262, D:E.299, D:H.437, H2O.23, H2O.41 ZN.14: 6 residues within 4Å: Chain D: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.13 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.93, D:D.262, D:D.262 ZN.15: 5 residues within 4Å: Chain D: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.510, D:H.530, D:C.532 ZN.16: 5 residues within 4Å: Chain D: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.496, D:T.498, D:C.499, D:C.519, D:C.522 ZN.17: 5 residues within 4Å: Chain E: D.262, E.298, E.299, H.437 Ligands: ZN.18 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.262, E:E.299, E:H.437, H2O.34 ZN.18: 6 residues within 4Å: Chain E: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.17 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.93, E:D.262, E:D.262 ZN.19: 5 residues within 4Å: Chain E: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.510, E:H.530, E:C.532 ZN.20: 5 residues within 4Å: Chain E: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.496, E:T.498, E:C.499, E:C.519, E:C.522 ZN.21: 5 residues within 4Å: Chain F: D.262, E.298, E.299, H.437 Ligands: ZN.22 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.262, F:E.299, F:H.437, H2O.27 ZN.22: 6 residues within 4Å: Chain F: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.21 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.93, F:D.262, H2O.33 ZN.23: 5 residues within 4Å: Chain F: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.510, F:H.530, F:C.532 ZN.24: 5 residues within 4Å: Chain F: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.496, F:T.498, F:C.499, F:C.519, F:C.522 ZN.25: 5 residues within 4Å: Chain G: D.262, E.298, E.299, H.437 Ligands: ZN.26 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.262, G:E.299, G:H.437 ZN.26: 6 residues within 4Å: Chain G: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.25 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.93, G:D.262, G:D.262 ZN.27: 5 residues within 4Å: Chain G: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.510, G:H.530, G:C.532 ZN.28: 5 residues within 4Å: Chain G: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:C.496, G:T.498, G:C.499, G:C.519, G:C.522 ZN.29: 5 residues within 4Å: Chain H: D.262, E.298, E.299, H.437 Ligands: ZN.30 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.262, H:E.299, H:H.437, H2O.67 ZN.30: 6 residues within 4Å: Chain H: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.29 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.93, H:D.262, H:D.262, H2O.46 ZN.31: 5 residues within 4Å: Chain H: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.510, H:H.530, H:C.532 ZN.32: 5 residues within 4Å: Chain H: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.496, H:T.498, H:C.499, H:C.519, H:C.522 ZN.33: 5 residues within 4Å: Chain I: D.262, E.298, E.299, H.437 Ligands: ZN.34 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.262, I:E.299, I:H.437, H2O.60 ZN.34: 6 residues within 4Å: Chain I: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.33 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.93, I:D.262, I:D.262 ZN.35: 5 residues within 4Å: Chain I: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.510, I:H.530, I:C.532 ZN.36: 5 residues within 4Å: Chain I: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:C.496, I:T.498, I:C.499, I:C.519, I:C.522 ZN.37: 5 residues within 4Å: Chain J: D.262, E.298, E.299, H.437 Ligands: ZN.38 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.262, J:E.299, J:H.437, H2O.53 ZN.38: 6 residues within 4Å: Chain J: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.37 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.93, J:D.262, J:D.262, H2O.57 ZN.39: 5 residues within 4Å: Chain J: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.510, J:H.530, J:C.532 ZN.40: 5 residues within 4Å: Chain J: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:C.496, J:T.498, J:C.499, J:C.519, J:C.522 ZN.41: 5 residues within 4Å: Chain K: D.262, E.298, E.299, H.437 Ligands: ZN.42 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.262, K:E.298, K:E.299, K:H.437, H2O.45 ZN.42: 6 residues within 4Å: Chain K: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.41 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.93, K:D.262, K:D.262, K:E.298 ZN.43: 5 residues within 4Å: Chain K: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.510, K:H.530, K:C.532 ZN.44: 5 residues within 4Å: Chain K: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:C.496, K:T.498, K:C.499, K:C.519, K:C.522 ZN.45: 5 residues within 4Å: Chain L: D.262, E.298, E.299, H.437 Ligands: ZN.46 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.262, L:E.299, L:H.437, H2O.18 ZN.46: 6 residues within 4Å: Chain L: H.93, D.262, E.298, E.299, D.343 Ligands: ZN.45 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.93, L:D.262, L:D.262, H2O.69 ZN.47: 5 residues within 4Å: Chain L: C.510, K.512, C.513, H.530, C.532 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.510, L:H.530, L:C.532 ZN.48: 5 residues within 4Å: Chain L: C.496, T.498, C.499, C.519, C.522 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.496, L:T.498, L:C.499, L:C.519, L:C.522

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.Y. et al., Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. Embo J. (2021)

Release Date

2021-07-14

Peptides

Aspartyl aminopeptidase 1,ZZ-type zinc finger-containing protein P35G2.11c,Maltose/maltodextrin-binding periplasmic protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
I

F
K

G
M

H
O

I
Q

J
S

K
V

L
X

Aspartyl aminopeptidase 1,ZZ-type zinc finger-containing protein P35G2.11c,Maltose/maltodextrin-binding periplasmic protein