1I2T

X-RAY STRUCTURE OF THE HUMAN HYPERPLASTIC DISCS PROTEIN: AN ORTHOLOG OF THE C-TERMINAL DOMAIN OF POLY(A)-BINDING PROTEIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

X-ray structure of the human hyperplastic discs protein: an ortholog of the C-terminal domain of poly(A)-binding protein.

Deo, R.C., Sonenberg, N., Burley, S.K.

(2001) Proc Natl Acad Sci U S A 98: 4414-4419

  • DOI: 10.1073/pnas.071552198
  • Primary Citation of Related Structures:  
    1I2T

  • PubMed Abstract: 

    • The poly(A)-binding protein (PABP) recognizes the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilization/degradation. PABP is a modular protein, with four N-terminal RNA-binding domains and an extensive C terminus ...

    The poly(A)-binding protein (PABP) recognizes the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilization/degradation. PABP is a modular protein, with four N-terminal RNA-binding domains and an extensive C terminus. The C-terminal region of PABP is essential for normal growth in yeast and has been implicated in mediating PABP homo-oligomerization and protein-protein interactions. A small, proteolytically stable, highly conserved domain has been identified within this C-terminal segment. Remarkably, this domain is also present in the hyperplastic discs protein (HYD) family of ubiquitin ligases. To better understand the function of this conserved region, an x-ray structure of the PABP-like segment of the human HYD protein has been determined at 1.04-A resolution. The conserved domain adopts a novel fold resembling a right-handed supercoil of four alpha-helices. Sequence profile searches and comparative protein structure modeling identified a small ORF from the Arabidopsis thaliana genome that encodes a structurally similar but distantly related PABP/HYD domain. Phylogenetic analysis of the experimentally determined (HYD) and homology modeled (PABP) protein surfaces revealed a conserved feature that may be responsible for binding to a PABP interacting protein, Paip1, and other shared interaction partners.

    Organizational Affiliation: 

    Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYD PROTEINA61Homo sapiensMutation(s): 0 
Gene Names: HYD, UBR5, EDD, EDD1, KIAA0896
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95071 (Homo sapiens)
Explore O95071 
Go to UniProtKB:  O95071
PHAROS:  O95071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95071
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.969α = 90
b = 38.166β = 90
c = 51.062γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Structure summary