6G9X

Crystal structure of a MFS transporter at 2.54 Angstroem resolution

PDB DOI: https://doi.org/10.2210/pdb6G9X/pdb

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

Deposited: 2018-04-11 Released: 2019-07-03
Deposition Author(s): Kalbermatter, D., Bosshart, P., Bonetti, S., Fotiadis, D.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.254
R-Value Work: 0.217
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

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.

Macromolecule Content

Total Structure Weight: 94.39 kDa
Atom Count: 5,932
Modelled Residue Count: 764
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0LNN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BNG Query on BNG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain K [auth A]	K [auth A] L [auth A] M [auth A] U [auth B] V [auth B] K [auth A], L [auth A], M [auth A], U [auth B], V [auth B], W [auth B]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain G [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], N [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
JKE Query on JKE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B]	I [auth A], T [auth B]	2-sulfanylbenzoic acid C₇ H₆ O₂ S NBOMNTLFRHMDEZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.254
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.765	α = 90
b = 200.539	β = 90
c = 64.561	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
autoPROC	data scaling
CRANK2	phasing
BUCCANEER	model building
Coot	model building
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

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

Revision History (Full details and data files)

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

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Help and Resources

6G9X

Crystal structure of a MFS transporter at 2.54 Angstroem resolution

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)