SMTL ID : 8h35.1

Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-8-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain E: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.42, E:C.45, E:H.80, E:C.83 ZN.2: 4 residues within 4Å: Chain E: C.75, H.77, C.94, D.97 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.75, E:H.77, E:C.94, E:D.97 ZN.3: 5 residues within 4Å: Chain A: R.751 Chain E: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.53, E:C.56, E:C.68, E:H.82 ZN.4: 4 residues within 4Å: Chain F: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.42, F:C.45, F:H.80, F:C.83 ZN.5: 4 residues within 4Å: Chain F: C.75, H.77, C.94, D.97 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.75, F:H.77, F:C.94, F:D.97, F:D.97 ZN.6: 5 residues within 4Å: Chain B: R.751 Chain F: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.53, F:C.56, F:C.68, F:H.82 ZN.7: 4 residues within 4Å: Chain K: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.42, K:C.45, K:H.80, K:C.83 ZN.8: 3 residues within 4Å: Chain K: C.75, H.77, C.94 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.75, K:H.77 ZN.9: 5 residues within 4Å: Chain I: R.751 Chain K: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.53, K:C.56, K:C.68, K:H.82 ZN.10: 4 residues within 4Å: Chain L: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.42, L:C.45, L:H.80, L:C.83 ZN.11: 4 residues within 4Å: Chain L: C.75, H.77, C.94, D.97 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.75, L:H.77, L:C.94, L:D.97, L:D.97 ZN.12: 5 residues within 4Å: Chain J: R.751 Chain L: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.53, L:C.56, L:C.68, L:H.82 ZN.13: 4 residues within 4Å: Chain Q: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.42, Q:C.45, Q:H.80, Q:C.83 ZN.14: 4 residues within 4Å: Chain Q: C.75, H.77, C.94, D.97 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.75, Q:H.77, Q:C.94, Q:D.97 ZN.15: 5 residues within 4Å: Chain O: R.751 Chain Q: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.53, Q:C.56, Q:C.68, Q:H.82 ZN.16: 4 residues within 4Å: Chain R: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.42, R:C.45, R:H.80, R:C.83 ZN.17: 3 residues within 4Å: Chain R: C.75, H.77, C.94 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:C.75, R:H.77 ZN.18: 5 residues within 4Å: Chain P: R.751 Chain R: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.53, R:C.56, R:C.68, R:H.82 ZN.19: 4 residues within 4Å: Chain W: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.42, W:C.45, W:H.80, W:C.83 ZN.20: 4 residues within 4Å: Chain W: C.75, H.77, C.94, D.97 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.75, W:H.77, W:C.94, W:D.97 ZN.21: 5 residues within 4Å: Chain S: R.751 Chain W: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.53, W:C.56, W:C.68, W:H.82 ZN.22: 4 residues within 4Å: Chain X: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.42, X:C.45, X:H.80, X:C.83 ZN.23: 4 residues within 4Å: Chain X: C.75, H.77, C.94, D.97 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:C.75, X:H.77, X:C.94, X:D.97, X:D.97 ZN.24: 5 residues within 4Å: Chain V: R.751 Chain X: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.53, X:C.56, X:C.68, X:H.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Y. et al., Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3 KBTBD2. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-10-11

Peptides

Cullin-3: ABIJOPSV
Kelch repeat and BTB domain-containing protein 2: CDGHMNTU
E3 ubiquitin-protein ligase RBX1: EFKLQRWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

I
I

J
H

O
M

P
O

S
T

V
V

C
A

D
B

G
G

H
J

M
P

N
N

T
S

U
U

E
E

F
D

K
L

L
K

Q
R

R
Q

W
W

X
X

Cullin-3

Kelch repeat and BTB domain-containing protein 2

E3 ubiquitin-protein ligase RBX1

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