Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.13 kDa 
• Atom Count: 4983 
• Modelled Residue Count: 625 
• Deposited Residue Count: 707 
• Unique protein chains: 2

4AP2

Crystal structure of the human KLHL11-Cul3 complex at 2.8A resolution

• DOI: 10.2210/pdb4AP2/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-03-30 Released: 2012-05-09 
• Deposition Author(s): Canning, P., Cooper, C.D.O., Krojer, T., Filippakopoulos, P., Ayinampudi, V., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Bullock, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

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
• Primary Citation of Related Structures:  
  2VPJ, 3II7, 4APF, 4ASC, 2XN4, 4AP2


• 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	Image
KELCH-LIKE PROTEIN 11	A	297	Homo sapiens	Mutation(s): 0  Gene Names: KLHL11
Find proteins for Q9NVR0 (Homo sapiens) Explore Q9NVR0  Go to UniProtKB:  Q9NVR0
NIH Common Fund Data Resources
PHAROS:  Q9NVR0 GTEx:  ENSG00000178502

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CULLIN-3	B	410	Homo sapiens	Mutation(s): 2  Gene Names: CUL3, KIAA0617
Find proteins for Q13618 (Homo sapiens) Explore Q13618  Go to UniProtKB:  Q13618
NIH Common Fund Data Resources
PHAROS:  Q13618 GTEx:  ENSG00000036257

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	A, B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.536	α = 90
b = 40.162	β = 107.36
c = 234.758	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-30 
• Released Date: 2012-05-09 
Deposition Author(s): Canning, P., Cooper, C.D.O., Krojer, T., Filippakopoulos, P., Ayinampudi, V., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Bullock, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2013-02-06
  Changes: Database references, Structure summary
• Version 1.2: 2013-03-27
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary