Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 33.02 kDa 
• Atom Count: 2330 
• Residue Count: 289 
• Unique protein chains: 1

2VPJ

Crystal structure of the Kelch domain of human KLHL12

• DOI: 10.2210/pdb2VPJ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-29 Released: 2008-03-18 
• Deposition Author(s): Keates, T., Pike, A.C.W., Bullock, A.N., Salah, E., Filippakopoulos, P., Roos, A.K., von Delft, F., Savitsky, P., Weigelt, J., Edwards, A., Arrowsmith, C.H., Bountra, C., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.222 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 

Literature

Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases.

Canning, P., Cooper, C.D.O., Krojer, T., Murray, J.W., Pike, A.C.W., Chaikuad, A., Keates, T., Thangaratnarajah, C., Hojzan, V., Marsden, B.D., Gileadi, O., Knapp, S., von Delft, F., Bullock, A.N.

(2013) J Biol Chem 288: 7803

• PubMed: 23349464 
• DOI: 10.1074/jbc.M112.437996
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Cullin-RING ligases are multisubunit E3 ubiquitin ligases that recruit substrate-specific adaptors to catalyze protein ubiquitylation. Cul3-based Cullin-RING ligases are uniquely associated with BTB adaptors that incorporate homodimerization, Cul3 assembly, and substrate recognition into a single multidomain protein, of which the best known are BTB-BACK-Kelch domain proteins, including KEAP1. Cul3 assembly requires a BTB protein "3-box" motif, analogous to the F-box and SOCS box motifs of other Cullin-based E3s. To define the molecular basis for this assembly and the overall architecture of the E3, we determined the crystal structures of the BTB-BACK domains of KLHL11 both alone and in complex with Cul3, along with the Kelch domain structures of KLHL2 (Mayven), KLHL7, KLHL12, and KBTBD5. We show that Cul3 interaction is dependent on a unique N-terminal extension sequence that packs against the 3-box in a hydrophobic groove centrally located between the BTB and BACK domains. Deletion of this N-terminal region results in a 30-fold loss in affinity. The presented data offer a model for the quaternary assembly of this E3 class that supports the bivalent capture of Nrf2 and reveals potential new sites for E3 inhibitor design.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
KELCH-LIKE PROTEIN 12	A	301	Homo sapiens	Mutation(s): 0  Gene Names: KLHL12, C3IP1
Find proteins for Q53G59 (Homo sapiens) Explore Q53G59  Go to UniProtKB:  Q53G59
NIH Common Fund Data Resources
PHAROS  Q53G59 GTEx  ENSG00000117153

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.222 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.637	α = 90
b = 61.546	β = 111.75
c = 45.523	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-29 
• Released Date: 2008-03-18 
Deposition Author(s): Keates, T., Pike, A.C.W., Bullock, A.N., Salah, E., Filippakopoulos, P., Roos, A.K., von Delft, F., Savitsky, P., Weigelt, J., Edwards, A., Arrowsmith, C.H., Bountra, C., Knapp, S.

Revision History 

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2013-02-06
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2013-03-27
  Changes: Database references
• Version 1.4: 2018-01-24
  Changes: Database references