Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 105.40 kDa 
• Atom Count: 6472 
• Modelled Residue Count: 854 
• Deposited Residue Count: 950 
• Unique protein chains: 3

3ZKJ

Crystal Structure of Ankyrin Repeat and Socs Box-Containing Protein 9 (Asb9) in Complex with Elonginb and Elonginc

• DOI: 10.2210/pdb3ZKJ/pdb
• Entry: 3ZKJ supersedes: 2XAI

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


• Deposited: 2013-01-23 Released: 2013-01-30 
• Deposition Author(s): Muniz, J.R.C., Guo, K., Zhang, Y., Ayinampudi, V., Savitsky, P., Keates, T., Filippakopoulos, P., Vollmar, M., Yue, W.W., Krojer, T., Ugochukwu, E., von Delft, F., Knapp, S., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.265 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Molecular Architecture of the Ankyrin Socs Box Family of Cul5-Dependent E3 Ubiquitin Ligases

Muniz, J.R.C., Guo, K., Kershaw, N.J., Ayinampudi, V., von Delft, F., Babon, J.J., Bullock, A.N.

(2013) J Mol Biol 425: 3166

• PubMed: 23806657 
• DOI: 10.1016/j.jmb.2013.06.015
• Primary Citation of Related Structures:  
  2WZK, 3ZKJ


• PubMed Abstract: 
  

Multi-subunit Cullin-RING E3 ligases often use repeat domain proteins as substrate-specific adaptors. Structures of these macromolecular assemblies are determined for the F-box-containing leucine-rich repeat and WD40 repeat families, but not for the suppressor of cytokine signaling (SOCS)-box-containing ankyrin repeat proteins (ASB1-18), which assemble with Elongins B and C and Cul5. We determined the crystal structures of the ternary complex of ASB9-Elongin B/C as well as the interacting N-terminal domain of Cul5 and used structural comparisons to establish a model for the complete Cul5-based E3 ligase. The structures reveal a distinct architecture of the ASB9 complex that positions the ankyrin domain coaxial to the SOCS box-Elongin B/C complex and perpendicular to other repeat protein complexes. This alternative architecture appears favorable to present the ankyrin domain substrate-binding site to the E2-ubiquitin, while also providing spacing suitable for bulky ASB9 substrates, such as the creatine kinases. The presented Cul5 structure also differs from previous models and deviates from other Cullins via a rigid-body rotation between Cullin repeats. This work highlights the adaptability of repeat domain proteins as scaffolds in substrate recognition and lays the foundation for future structure-function studies of this important E3 family.

---

Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANKYRIN REPEAT AND SOCS BOX PROTEIN 9	A, D	261	Homo sapiens	Mutation(s): 0  Gene Names: ASB9
Find proteins for Q96DX5 (Homo sapiens) Explore Q96DX5  Go to UniProtKB:  Q96DX5
NIH Common Fund Data Resources
PHAROS:  Q96DX5 GTEx:  ENSG00000102048

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1	B, E	96	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
NIH Common Fund Data Resources
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2	C, F	118	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
NIH Common Fund Data Resources
PHAROS:  Q15370 GTEx:  ENSG00000103363

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	A, D	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	A, F	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.265 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.86	α = 90
b = 110.74	β = 90
c = 113.41	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-23 
• Released Date: 2013-01-30 
Deposition Author(s): Muniz, J.R.C., Guo, K., Zhang, Y., Ayinampudi, V., Savitsky, P., Keates, T., Filippakopoulos, P., Vollmar, M., Yue, W.W., Krojer, T., Ugochukwu, E., von Delft, F., Knapp, S., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.
• This entry supersedes: 2XAI

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references, Other, Refinement description, Structure summary
• Version 1.2: 2013-07-10
  Changes: Database references
• Version 1.3: 2013-08-28
  Changes: Database references
• Version 1.4: 2018-01-24
  Changes: Database references