2COM

The solution structure of the SWIRM domain of human LSD1


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of the SWIRM domain of human histone demethylase LSD1

Tochio, N.Umehara, T.Koshiba, S.Inoue, M.Yabuki, T.Aoki, M.Seki, E.Watanabe, S.Tomo, Y.Hanada, M.Ikari, M.Sato, M.Terada, T.Nagase, T.Ohara, O.Shirouzu, M.Tanaka, A.Kigawa, T.Yokoyama, S.

(2006) Structure 14: 457-468

  • DOI: 10.1016/j.str.2005.12.004
  • Primary Citation of Related Structures:  
    2COM

  • PubMed Abstract: 
  • SWIRM is an evolutionarily conserved domain involved in several chromatin-modifying complexes. Recently, the LSD1 protein, which bears a SWIRM domain, was found to be a demethylase for Lys4-methylated histone H3. Here, we report a solution structure of the SWIRM domain of human LSD1 ...

    SWIRM is an evolutionarily conserved domain involved in several chromatin-modifying complexes. Recently, the LSD1 protein, which bears a SWIRM domain, was found to be a demethylase for Lys4-methylated histone H3. Here, we report a solution structure of the SWIRM domain of human LSD1. It forms a compact fold composed of 6 alpha helices, in which a 20 amino acid long helix (alpha4) is surrounded by 5 other short helices. The SWIRM domain structure could be divided into the N-terminal part (alpha1-alpha3) and the C-terminal part (alpha4-alpha6), which are connected to each other by a salt bridge. While the N-terminal part forms a SWIRM-specific structure, the C-terminal part adopts a helix-turn-helix (HTH)-related fold. We discuss a model in which the SWIRM domain acts as an anchor site for a histone tail.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1A124Homo sapiensMutation(s): 0 
Gene Names: LSD1KDM1AAOF2KDM1KIAA0601
EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens)
Explore O60341 
Go to UniProtKB:  O60341
PHAROS:  O60341
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60341
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: target function,structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Data collection, Database references, Derived calculations