6HCL

Crystal structure of a MFS transporter with Ligand at 2.69 Angstroem resolution

• PDB DOI: https://doi.org/10.2210/pdb6HCL/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Syntrophobacter fumaroxidans MPOB
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2018-08-15 Released: 2019-07-03 
• Deposition Author(s): Kalbermatter, D., Bosshart, P., Bonetti, S., Fotiadis, D.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 

Starting Model: experimental

Literature

Mechanistic basis of L-lactate transport in the SLC16 solute carrier family.

Bosshart, P.D., Kalbermatter, D., Bonetti, S., Fotiadis, D.

(2019) Nat Commun 10: 2649-2649

• PubMed: 31201333 
• DOI: https://doi.org/10.1038/s41467-019-10566-6
• Primary Citation of Related Structures:  
  6G9X, 6HCL


• PubMed Abstract: 
  

  In human and other mammalian cells, transport of L-lactate across plasma membranes is mainly catalyzed by monocarboxylate transporters (MCTs) of the SLC16 solute carrier family. MCTs play an important role in cancer metabolism and are promising targets for tumor treatment. Here, we report the crystal structures of an SLC16 family homologue with two different bound ligands at 2.54 and 2.69 Å resolution. The structures show the transporter in the pharmacologically relevant outward-open conformation. Structural information together with a detailed structure-based analysis of the transport function provide important insights into the molecular working mechanisms of ligand binding and L-lactate transport.

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Organizational Affiliation: 

Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.18 kDa 
• Atom Count: 5,771 
• Modelled Residue Count: 761 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major facilitator superfamily MFS_1	A, B	420	Syntrophobacter fumaroxidans MPOB	Mutation(s): 0  Gene Names: Sfum_3364 Membrane Entity: Yes
UniProt
Find proteins for A0LNN5 (Syntrophobacter fumaroxidans (strain DSM 10017 / MPOB)) Explore A0LNN5  Go to UniProtKB:  A0LNN5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG	D [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
2OP	C [auth A], E [auth B], F [auth B]	(2S)-2-HYDROXYPROPANOIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.423	α = 90
b = 200.016	β = 90
c = 63.323	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Kalbermatter, D., Bosshart, P., Bonetti, S., Fotiadis, D.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary