Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.00 kDa 
• Atom Count: 3477 
• Modelled Residue Count: 448 
• Deposited Residue Count: 455 
• Unique protein chains: 1

5XJJ

Crystal structure of a MATE family protein

• PDB DOI: 10.2210/pdb5XJJ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Camelina sativa
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-05-02 Released: 2017-09-20 
• Deposition Author(s): Tanaka, Y., Tsukazaki, T., Iwaki, S.
• Funding Organization(s): JSPS/MEXT, PRESTO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.296 
• R-Value Work: 0.239 
• R-Value Observed: 0.244 

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

• PubMed: 28877507 
• DOI: 10.1016/j.str.2017.07.009
• Primary Citation of 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.

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Organizational Affiliation: 

Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
multi drug efflux transporter	A	455	Camelina sativa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2D0TCI5 (Camelina sativa) Explore A0A2D0TCI5  Go to UniProtKB:  A0A2D0TCI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	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 
• R-Value Work: 0.239 
• R-Value Observed: 0.244 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.71	α = 90
b = 69.89	β = 90
c = 117.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data collection
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-02 
• Released Date: 2017-09-20 
Deposition Author(s): Tanaka, Y., Tsukazaki, T., Iwaki, S.

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Funding Organization	Location	Grant Number
JSPS/MEXT	Japan	JP26119007, JP26291023, JP16K14713, JP15H01537, JP15K06972
PRESTO	Japan	JPMJPR12L3

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Database references