4WQO

Structure of VHL-EloB-EloC-Cul2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into Cullin-RING E3 Ubiquitin Ligase Recruitment: Structure of the VHL-EloBC-Cul2 Complex.

Nguyen, H.C.Yang, H.Fribourgh, J.L.Wolfe, L.S.Xiong, Y.

(2015) Structure 23: 441-449

  • DOI: 10.1016/j.str.2014.12.014
  • Primary Citation of Related Structures:  
    4WQO

  • PubMed Abstract: 
  • The von Hippel-Lindau tumor suppressor protein (VHL) recruits a Cullin 2 (Cul2) E3 ubiquitin ligase to downregulate HIF-1α, an essential transcription factor for the hypoxia response. Mutations in VHL lead to VHL disease and renal cell carcinomas. Inhibition of this pathway to upregulate erythropoietin production is a promising new therapy to treat ischemia and chronic anemia ...

    The von Hippel-Lindau tumor suppressor protein (VHL) recruits a Cullin 2 (Cul2) E3 ubiquitin ligase to downregulate HIF-1α, an essential transcription factor for the hypoxia response. Mutations in VHL lead to VHL disease and renal cell carcinomas. Inhibition of this pathway to upregulate erythropoietin production is a promising new therapy to treat ischemia and chronic anemia. Here, we report the crystal structure of VHL bound to a Cul2 N-terminal domain, Elongin B, and Elongin C (EloC). Cul2 interacts with both the VHL BC box and cullin box and a novel EloC site. Comparison with other cullin E3 ligase structures shows that there is a conserved, yet flexible, cullin recognition module and that cullin selectivity is influenced by distinct electrostatic interactions. Our structure provides a structural basis for the study of the pathogenesis of VHL disease and rationale for the design of novel compounds that may modulate cullin-substrate receptor interactions.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA. Electronic address: yong.xiong@yale.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Von Hippel-Lindau disease tumor suppressorA233Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
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Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
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UniProt GroupP40337
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor B polypeptide 2B118Homo sapiensMutation(s): 0 
Gene Names: TCEB2ELOB
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor B polypeptide 1C96Homo sapiensMutation(s): 0 
Gene Names: TCEB1ELOC
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Find proteins for Q15369 (Homo sapiens)
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PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-2D186Homo sapiensMutation(s): 0 
Gene Names: CUL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens)
Explore Q13617 
Go to UniProtKB:  Q13617
PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.278α = 90
b = 108.278β = 90
c = 213.768γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy