5YCK | pdb_00005yck

Crystal structure of a MATE family protein derived from Camelina sativa at 2.3 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.254 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein

Tanaka, Y.Iwaki, S.Tsukazaki, T.

(2017) Structure 25: 1455-1460.e2

  • DOI: https://doi.org/10.1016/j.str.2017.07.009
  • Primary Citation Related Structures: 
    5XJJ, 5YCK

  • PubMed Abstract: 

    The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins. Here, we describe the crystal structure of a MATE protein from the plant Camelina sativa at 2.9 Å resolution. Two sets of six transmembrane α helices, assembled pseudo-symmetrically, possess a negatively charged internal pocket with an outward-facing shape. The crystal structure provides insight into the diversity of plant MATE proteins and their substrate recognition and transport through the membrane.


  • Organizational Affiliation
    • Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.

Macromolecule Content 

  • Total Structure Weight: 52.67 kDa 
  • Atom Count: 3,614 
  • Modeled Residue Count: 450 
  • Deposited Residue Count: 471 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
multi drug efflux transporter471Camelina sativaMutation(s): 0 
Gene Names: false flax
Membrane Entity: Yes 
UniProt
Find proteins for R0G998 (Capsella rubella)
Explore R0G998 
Go to UniProtKB:  R0G998
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR0G998
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.65α = 90
b = 69.24β = 90
c = 116.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description