5XJJ | pdb_00005xjj

Crystal structure of a MATE family protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.296 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5XJJ

Ligand Structure Quality Assessment 


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: 50 kDa 
  • Atom Count: 3,477 
  • Modeled Residue Count: 448 
  • Deposited Residue Count: 455 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
multi drug efflux transporter455Camelina sativaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D0TCI5 (Camelina sativa)
Explore A0A2D0TCI5 
Go to UniProtKB:  A0A2D0TCI5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCI5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC

Query on OLC



Download:Ideal Coordinates CCD File
B [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.296 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.71α = 90
b = 69.89β = 90
c = 117.6γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata collection
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS/MEXTJapanJP26119007, JP26291023, JP16K14713, JP15H01537, JP15K06972
PRESTOJapanJPMJPR12L3

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description