4YTW

Crystal structure of Ups1-Mdm35 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and mechanistic insights into phospholipid transfer by Ups1-Mdm35 in mitochondria.

Watanabe, Y.Tamura, Y.Kawano, S.Endo, T.

(2015) Nat Commun 6: 7922-7922

  • DOI: https://doi.org/10.1038/ncomms8922
  • Primary Citation of Related Structures:  
    4YTV, 4YTW, 4YTX

  • PubMed Abstract: 

    Eukaryotic cells are compartmentalized into membrane-bounded organelles whose functions rely on lipid trafficking to achieve membrane-specific compositions of lipids. Here we focused on the Ups1-Mdm35 system, which mediates phosphatidic acid (PA) transfer between the outer and inner mitochondrial membranes, and determined the X-ray structures of Mdm35 and Ups1-Mdm35 with and without PA. The Ups1-Mdm35 complex constitutes a single domain that has a deep pocket and flexible Ω-loop lid. Structure-based mutational analyses revealed that a basic residue at the pocket bottom and the Ω-loop lid are important for PA extraction from the membrane following Ups1 binding. Ups1 binding to the membrane is enhanced by the dissociation of Mdm35. We also show that basic residues around the pocket entrance are important for Ups1 binding to the membrane and PA extraction. These results provide a structural basis for understanding the mechanism of PA transfer between mitochondrial membranes.


  • Organizational Affiliation

    1] Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan [2] JST/CREST, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan [3] JST/CREST, Research Center for Materials Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial distribution and morphology protein 35
A, C
81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MDM35YKL053C-A
UniProt
Find proteins for O60200 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O60200 
Go to UniProtKB:  O60200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60200
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein UPS1, mitochondrial
B, D
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UPS1YLR193C
UniProt
Find proteins for Q05776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05776 
Go to UniProtKB:  Q05776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05776
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.75α = 90
b = 71.746β = 95.02
c = 87.607γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
PHENIXmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations