7DQK | pdb_00007dqk

A nicotine MATE transporter, Nicotiana tabacum MATE2 (NtMATE2)

• PDB DOI: https://doi.org/10.2210/pdb7DQK/pdb

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


• Deposited: 2020-12-24 Released: 2021-06-09 
• Deposition Author(s): Tanaka, Y., Tsukazaki, T., Sasaki, A., Iwaki, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

Starting Model: experimental

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

• PubMed: 34050946 
• 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.

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Organizational Affiliation: 

Nara Institute of Science and Technology, Ikoma, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.85 kDa 
• Atom Count: 7,383 
• Modelled Residue Count: 955 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DETOXIFICATION	A, B	510	Nicotiana tabacum	Mutation(s): 0  Gene Names: NtMATE2, LOC107807968 Membrane Entity: Yes
UniProt
Find proteins for A3KDM5 (Nicotiana tabacum) Explore A3KDM5  Go to UniProtKB:  A3KDM5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	D [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	E [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61	α = 90
b = 89.37	β = 90
c = 228.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Tanaka, Y., Tsukazaki, T., Sasaki, A., Iwaki, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• 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