5GYD

Crystal Structure of Mdm12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Literature

Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex

Jeong, H.Park, J.Lee, C.

(2016) EMBO Rep 17: 1857-1871

  • DOI: https://doi.org/10.15252/embr.201642706
  • Primary Citation of Related Structures:  
    5GYD, 5GYK

  • PubMed Abstract: 

    The endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex that plays a tethering role in physically connecting ER and mitochondria membranes. The ERMES complex is composed of Mdm12, Mmm1, and Mdm34, which have a SMP domain in common, and Mdm10. Here, we report the crystal structure of S. cerevisiae Mdm12. The Mdm12 forms a dimeric SMP structure through domain swapping of the β1-strand comprising residues 1-7. Biochemical experiments reveal a phospholipid-binding site located along a hydrophobic channel of the Mdm12 structure and that Mdm12 might have a binding preference for glycerophospholipids harboring a positively charged head group. Strikingly, both full-length Mdm12 and Mdm12 truncated to exclude the disordered region (residues 74-114) display the same organization in the asymmetric unit, although they crystallize as a tetramer and hexamer, respectively. Taken together, these studies provide a novel understanding of the overall organization of SMP domains in the ERMES complex, indicating that Mdm12 interacts with Mdm34 through head-to-head contact, and with Mmm1 through tail-to-tail contact of SMP domains.


  • Organizational Affiliation

    Department of Biological Sciences, School of Life Sciences Ulsan National Institute of Science and Technology, Ulsan, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial distribution and morphology protein 12
A, B, C, D
272Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MDM12YOL009C
UniProt
Find proteins for Q92328 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q92328 
Go to UniProtKB:  Q92328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92328
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.592α = 90
b = 219.073β = 90
c = 73.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
AutoSolphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 2.0: 2024-03-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary