7DQK

A nicotine MATE transporter, Nicotiana tabacum MATE2 (NtMATE2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.264 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of a nicotine MATE transporter provide insight into its mechanism of substrate transport.

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

(2021) FEBS Lett 595: 1902-1913

  • DOI: https://doi.org/10.1002/1873-3468.14136
  • Primary Citation of Related Structures:  
    7DQK

  • PubMed Abstract: 

    A transporter of the multidrug and toxic compound extrusion (MATE) family, Nicotiana tabacum MATE2 (NtMATE2), is located in the vacuole membrane of the tobacco plant root and is involved in the transportation of nicotine, a secondary or specialized metabolic compound in Solanaceae. Here, we report the crystal structures of NtMATE2 in its outward-facing forms. The overall structure has a bilobate V-shape with pseudo-symmetrical assembly of the N- and C-lobes. In one crystal structure, the C-lobe cavity of NtMATE2 interacts with an unidentified molecule that may partially mimic a substrate. In addition, NtMATE2-specific conformational transitions imply that an unprecedented movement of the transmembrane α-helix 7 is related to the release of the substrate into the vacuolar lumen.


  • Organizational Affiliation

    Nara Institute of Science and Technology, Ikoma, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein DETOXIFICATION
A, B
510Nicotiana tabacumMutation(s): 0 
Gene Names: NtMATE2LOC107807968
Membrane Entity: Yes 
UniProt
Find proteins for A3KDM5 (Nicotiana tabacum)
Explore A3KDM5 
Go to UniProtKB:  A3KDM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3KDM5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61α = 90
b = 89.37β = 90
c = 228.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description