5IX2

Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and unmodified H3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 113: E5108-E5116

  • DOI: 10.1073/pnas.1609709113
  • Primary Citation of Related Structures:  

  • 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 h ...

    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

    Molecular Biology Institute, University of California, Los Angeles, CA 90095;,Department of Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; l.clemens-daxinger@lumc.nl pateld@mskcc.org jacobsen@ucla.edu.,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.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China;,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065; l.clemens-daxinger@lumc.nl pateld@mskcc.org jacobsen@ucla.edu.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095; Molecular Biology Institute, 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; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MORC family CW-type zinc finger protein 3
A, B
451Mus musculusMutation(s): 0 
Gene Names: Morc3 (Nxp2, Zcwcc3)
Find proteins for F7BJB9 (Mus musculus)
Go to UniProtKB:  F7BJB9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide from Histone H3.1
P, Q
32Mus musculusMutation(s): 0 
Gene Names: H3c1, H3c8, H3c10, H3c11 (H3a, Hist1h3a, H3.1-221, H3g, Hist1h3g, H3.1-291, H3h, Hist1h3h, H3.1-I, H3i, Hist1h3i)
Find proteins for P68433 (Mus musculus)
Go to UniProtKB:  P68433
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 112.202α = 90.00
b = 147.542β = 90.00
c = 173.611γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection, Database references, Derived calculations