5VKZ

Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies.

AhYoung, A.P.Lu, B.Cascio, D.Egea, P.F.

(2017) Biochem. Biophys. Res. Commun. 488: 129-135

  • DOI: 10.1016/j.bbrc.2017.05.021

  • PubMed Abstract: 
  • Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum - Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-v ...

    Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum - Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.


    Related Citations: 
    • Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex.
      Jeong, H.,Park, J.,Lee, C.
      (2016) EMBO Rep. 17: 1857
    • Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly.
      AhYoung, A.P.,Jiang, J.,Zhang, J.,Khoi Dang, X.,Loo, J.A.,Zhou, Z.H.,Egea, P.F.
      (2015) Proc. Natl. Acad. Sci. U.S.A. 112: E3179


    Organizational Affiliation

    Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial distribution and morphology protein 12
A, B
275Saccharomyces cerevisiae (strain AWRI1631)Mutation(s): 0 
Gene Names: MDM12
Find proteins for B5VRP4 (Saccharomyces cerevisiae (strain AWRI1631))
Go to UniProtKB:  B5VRP4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.242 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.020α = 90.00
b = 116.020β = 90.00
c = 161.660γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release