5IX1

Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.1 of the entry. See complete history


Literature

Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin

Li, S.Yen, L.Pastor, W.A.Johnston, J.B.Du, J.Shew, C.J.Liu, W.Ho, J.Stender, B.Clark, A.T.Burlingame, A.L.Daxinger, L.Patel, D.J.Jacobsen, S.E.

(2016) Proc Natl Acad Sci U S A 113: E5108-E5116

  • DOI: 10.1073/pnas.1609709113
  • Primary Citation of Related Structures:  
    5IX1, 5IX2

  • PubMed Abstract: 
  • Microrchidia (MORC) proteins are GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPases that function in gene regulation in multiple organisms. Animal MORCs also contain CW-type zinc finger domains, which are known to bind to modified histones ...

    Microrchidia (MORC) proteins are GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPases that function in gene regulation in multiple organisms. Animal MORCs also contain CW-type zinc finger domains, which are known to bind to modified histones. We solved the crystal structure of the murine MORC3 ATPase-CW domain bound to the nucleotide analog AMPPNP (phosphoaminophosphonic acid-adenylate ester) and in complex with a trimethylated histone H3 lysine 4 (H3K4) peptide (H3K4me3). We observed that the MORC3 N-terminal ATPase domain forms a dimer when bound to AMPPNP. We used native mass spectrometry to show that dimerization is ATP-dependent, and that dimer formation is enhanced in the presence of nonhydrolyzable ATP analogs. The CW domain uses an aromatic cage to bind trimethylated Lys4 and forms extensive hydrogen bonds with the H3 tail. We found that MORC3 localizes to promoters marked by H3K4me3 throughout the genome, consistent with its binding to H3K4me3 in vitro. Our work sheds light on aspects of the molecular dynamics and function of MORC3.


    Organizational Affiliation

    Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095; Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 l.clemens-daxinger@lumc.nl pateld@mskcc.org jacobsen@ucla.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MORC family CW-type zinc finger protein 3A, B451Mus musculusMutation(s): 0 
Gene Names: Morc3Nxp2Zcwcc3
UniProt & NIH Common Fund Data Resources
Find proteins for F7BJB9 (Mus musculus)
Explore F7BJB9 
Go to UniProtKB:  F7BJB9
IMPC:  MGI:2136841
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide from Histone H3.1C [auth P], D [auth Q]15Mus musculusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P68433 (Mus musculus)
Explore P68433 
Go to UniProtKB:  P68433
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
F [auth A], I [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A], J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C [auth P], D [auth Q]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.353α = 90
b = 149.079β = 90
c = 173.473γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references