6MW7

Crystal structure of ATPase module of SMCHD1 bound to ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.194 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • PubMed Abstract: 
  • Variants in the gene  <i>SMCHD1 </i>, 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 SMCH ...

    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

    1Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA.,2Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA.,3Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Structural maintenance of chromosomes flexible hinge domain-containing protein 1
A, B, C, D
562Homo sapiensMutation(s): 1 
Gene Names: SMCHD1 (KIAA0650)
EC: 3.6.1.-
Find proteins for A6NHR9 (Homo sapiens)
Go to Gene View: SMCHD1
Go to UniProtKB:  A6NHR9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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: 2.194 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 108.756α = 90.00
b = 148.012β = 90.00
c = 191.138γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-3000data scaling
PHENIXrefinement
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited States--

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release