4XIZ

Structure of a phospholipid trafficking complex with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex

Yu, F.He, F.Yao, H.Wang, C.Wang, J.Li, J.Qi, X.Xue, H.Ding, J.Zhang, P.

(2015) EMBO Rep 16: 813-823

  • DOI: 10.15252/embr.201540137
  • Primary Citation of Related Structures:  
    4XHR, 4XIZ

  • PubMed Abstract: 
  • Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer ...

    Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer. Ups1 features a barrel-like structure consisting of an antiparallel β-sheet and three α-helices. Mdm35 adopts a three-helical clamp-like structure to wrap around Ups1 to form a stable complex. The β-sheet and α-helices of Ups1 form a long tunnel-like pocket to accommodate the substrate PA, and a short helix α2 acts as a lid to cover the pocket. The hydrophobic residues lining the pocket and helix α2 are critical for PA binding and transfer. In addition, a hydrophilic patch on the surface of Ups1 near the PA phosphate-binding site also plays an important role in the function of Ups1-Mdm35. Our study reveals the molecular basis of the function of Ups1-Mdm35 and sheds new light on the mechanism of intramitochondrial phospholipid transport by the MSF1/PRELI family proteins.


    Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China hwxue@sibs.ac.cn jpding@sibcb.ac.cn pengzhang01@sibs.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein UPS1, mitochondrialA, B170Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UPS1YLR193C
Membrane Entity: Yes 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial distribution and morphology protein 35C [auth M],
D [auth N]
70Saccharomyces 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LPP
Query on LPP

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.022α = 90
b = 74.123β = 95.14
c = 87.912γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2015-08-12
    Changes: Refinement description
  • Version 1.3: 2015-09-16
    Changes: Refinement description