1N27

Solution structure of the PWWP domain of mouse Hepatoma-derived growth factor, related protein 3


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution structure of the PWWP domain of the hepatoma-derived growth factor family.

Nameki, N.Tochio, N.Koshiba, S.Inoue, M.Yabuki, T.Aoki, M.Seki, E.Matsuda, T.Fujikura, Y.Saito, M.Ikari, M.Watanabe, M.Terada, T.Shirouzu, M.Yoshida, M.Hirota, H.Tanaka, A.Hayashizaki, Y.Guntert, P.Kigawa, T.Yokoyama, S.

(2005) Protein Sci 14: 756-764

  • DOI: 10.1110/ps.04975305
  • Primary Citation of Related Structures:  
    1N27

  • PubMed Abstract: 
  • Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins ...

    Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded beta-barrel with a PWWP-specific long loop connecting beta2 and beta3 (PR-loop), followed by a helical region including two alpha-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the beta1/beta2 loop (beta-beta arch) and the beta3/beta4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatoma-derived growth factor, related protein 3A96Mus musculusMutation(s): 0 
Gene Names: 4632410H03Hdgfl3Hdgfrp3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JMG7 (Mus musculus)
Explore Q9JMG7 
Go to UniProtKB:  Q9JMG7
IMPC:  MGI:1352760
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function 
  • OLDERADO: 1N27 Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance