SMTL ID : 8h34.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

18 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain E: C.55, C.58, H.93, C.96 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.55, E:C.58, E:H.93, E:C.96 ZN.2: 4 residues within 4Å: Chain E: C.88, H.90, C.107, D.110 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.88, E:H.90, E:C.107, E:D.110 ZN.3: 5 residues within 4Å: Chain A: R.751 Chain E: C.66, C.69, C.81, H.95 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.66, E:C.69, E:C.81, E:H.95 ZN.4: 4 residues within 4Å: Chain F: C.55, C.58, H.93, C.96 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.55, F:C.58, F:H.93, F:C.96 ZN.5: 4 residues within 4Å: Chain F: C.88, H.90, C.107, D.110 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.88, F:H.90, F:C.107, F:D.110, F:D.110 ZN.6: 5 residues within 4Å: Chain B: R.751 Chain F: C.66, C.69, C.81, H.95 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.66, F:C.69, F:C.81, F:H.95 ZN.7: 4 residues within 4Å: Chain K: C.55, C.58, H.93, C.96 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.55, K:C.58, K:H.93, K:C.96 ZN.8: 4 residues within 4Å: Chain K: C.88, H.90, C.107, D.110 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.88, K:H.90, K:C.107, K:D.110 ZN.9: 5 residues within 4Å: Chain G: R.751 Chain K: C.66, C.69, C.81, H.95 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.66, K:C.69, K:C.81, K:H.95 ZN.10: 4 residues within 4Å: Chain L: C.55, C.58, H.93, C.96 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.55, L:C.58, L:H.93, L:C.96 ZN.11: 4 residues within 4Å: Chain L: C.88, H.90, C.107, D.110 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.88, L:H.90, L:C.107, L:D.110, L:D.110 ZN.12: 5 residues within 4Å: Chain J: R.751 Chain L: C.66, C.69, C.81, H.95 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.66, L:C.69, L:C.81, L:H.95 ZN.13: 4 residues within 4Å: Chain Q: C.55, C.58, H.93, C.96 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.55, Q:C.58, Q:H.93, Q:C.96 ZN.14: 4 residues within 4Å: Chain Q: C.88, H.90, C.107, D.110 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.88, Q:H.90, Q:C.107, Q:D.110 ZN.15: 5 residues within 4Å: Chain O: R.751 Chain Q: C.66, C.69, C.81, H.95 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.66, Q:C.69, Q:C.81, Q:H.95 ZN.16: 4 residues within 4Å: Chain R: C.55, C.58, H.93, C.96 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.55, R:C.58, R:H.93, R:C.96 ZN.17: 4 residues within 4Å: Chain R: C.88, H.90, C.107, D.110 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:C.88, R:H.90, R:C.107, R:D.110, R:D.110 ZN.18: 5 residues within 4Å: Chain P: R.751 Chain R: C.66, C.69, C.81, H.95 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.66, R:C.69, R:C.81, R:H.95

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: ABGJOP
Kelch repeat and BTB domain-containing protein 2: CDHIMN
E3 ubiquitin-protein ligase RBX1: EFKLQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
O

G
C

J
F

O
I

P
H

C
P

D
N

H
A

I
B

M
G

N
J

E
R

F
Q

K
E

L
D

Q
L

R
K

Cullin-3

Kelch repeat and BTB domain-containing protein 2

E3 ubiquitin-protein ligase RBX1

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