3ZKJ

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

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

  • 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 supp ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANKYRIN REPEAT AND SOCS BOX PROTEIN 9 AD261Homo sapiensMutation(s): 0 
Gene Names: ASB9
Find proteins for Q96DX5 (Homo sapiens)
Explore Q96DX5 
Go to UniProtKB:  Q96DX5
NIH Common Fund Data Resources
PHAROS:  Q96DX5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 BE96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
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PHAROS:  Q15369
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 CF118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
NIH Common Fund Data Resources
PHAROS:  Q15370
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 102.86α = 90
b = 110.74β = 90
c = 113.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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