6OB6 | pdb_00006ob6

Human equilibrative nucleoside transporter-1, S-(4-nitrobenzyl)-6-thioinosine bound, merohedrally twinned

• PDB DOI: https://doi.org/10.2210/pdb6OB6/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2019-03-19 Released: 2019-07-03 
• Deposition Author(s): Wright, N.J., Lee, S.-Y.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.252 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Structures of human ENT1 in complex with adenosine reuptake inhibitors.

Wright, N.J., Lee, S.Y.

(2019) Nat Struct Mol Biol 26: 599-606

• PubMed: 31235912 
• DOI: https://doi.org/10.1038/s41594-019-0245-7
• Primary Citation Related Structures: 
  6OB6, 6OB7


• PubMed Abstract: 
  

  The human equilibrative nucleoside transporter 1 (hENT1), a member of the SLC29 family, plays crucial roles in adenosine signaling, cellular uptake of nucleoside for DNA and RNA synthesis, and nucleoside-derived anticancer and antiviral drug transport in humans. Because of its central role in adenosine signaling, it is the target of adenosine reuptake inhibitors (AdoRI), several of which are used clinically. Despite its importance in human physiology and pharmacology, the molecular basis of hENT1-mediated adenosine transport and its inhibition by AdoRIs are limited, owing to the absence of structural information on hENT1. Here, we present crystal structures of hENT1 in complex with two chemically distinct AdoRIs: dilazep and S-(4-nitrobenzyl)-6-thioinosine (NBMPR). Combined with mutagenesis study, our structural analyses elucidate two distinct inhibitory mechanisms exhibited on hENT1 and provide insight into adenosine recognition and transport. Our studies provide a platform for improved pharmacological intervention of adenosine and nucleoside analog drug transport by hENT1.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
Department of Biochemistry, Duke University Medical Center, Durham, NC, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 98.57 kDa 
• Atom Count: 5,512 
• Modeled Residue Count: 722 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Equilibrative nucleoside transporter 1	A, B	442	Homo sapiens	Mutation(s): 3  Gene Names: SLC29A1, ENT1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99808 (Homo sapiens) Explore Q99808  Go to UniProtKB:  Q99808
PHAROS:  Q99808 GTEx:  ENSG00000112759

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NBM	C [auth A], D [auth B]	6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine C17 H17 N5 O6 S DYCJFJRCWPVDHY-LSCFUAHRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NBM	BindingDB:  6OB6	Ki: min: 0.43, max: 0.71 (nM) from 3 assay(s)
		IC50: min: 1, max: 8.51 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.252 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.532	α = 90
b = 72.532	β = 90
c = 335.458	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Wright, N.J., Lee, S.-Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R35NS097241

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Database references
• Version 2.0: 2019-09-18
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2019-12-18
  Changes: Author supporting evidence
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description