6MW7

Crystal structure of ATPase module of SMCHD1 bound to ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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This is version 1.1 of the entry. See complete history


Literature

A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1.

Pedersen, L.C.Inoue, K.Kim, S.Perera, L.Shaw, N.D.

(2019) Commun Biol 2: 255-255

  • DOI: 10.1038/s42003-019-0499-y
  • Primary Citation of Related Structures:  
    6MW7

  • PubMed Abstract: 
  • Variants in the gene  SMCHD1 , which encodes an epigenetic repressor, have been linked to both congenital arhinia and a late-onset form of muscular dystrophy called facioscapulohumeral muscular dystrophy type 2 (FSHD2). This suggests that SMCHD1 has a diversity of functions in both developmental time and space ...

    Variants in the gene  SMCHD1 , which encodes an epigenetic repressor, have been linked to both congenital arhinia and a late-onset form of muscular dystrophy called facioscapulohumeral muscular dystrophy type 2 (FSHD2). This suggests that SMCHD1 has a diversity of functions in both developmental time and space. The C-terminal end of SMCHD1 contains an SMC-hinge domain which mediates homodimerization and chromatin association, whereas the molecular architecture of the N-terminal region, which harbors the GHKL-ATPase domain, is not well understood. We present the crystal structure of the human SMCHD1 N-terminal ATPase module bound to ATP as a functional dimer. The dimer is stabilized by a novel N-terminal ubiquitin-like fold and by a downstream transducer domain. While disease variants map to what appear to be critical interdomain/intermolecular interfaces, only the FSHD2-specific mutant constructs we tested consistently abolish ATPase activity and/or dimerization. These data suggest that the full functional profile of SMCHD1 has yet to be determined.


    Organizational Affiliation

    3Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114 USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes flexible hinge domain-containing protein 1A, B, C, D562Homo sapiensMutation(s): 1 
Gene Names: SMCHD1KIAA0650
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for A6NHR9 (Homo sapiens)
Explore A6NHR9 
Go to UniProtKB:  A6NHR9
PHAROS:  A6NHR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6NHR9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.756α = 90
b = 148.012β = 90
c = 191.138γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence