8TZ3

Cryo-EM structure of bovine concentrative nucleoside transporter 3 in complex with GS-441524, consensus reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Antiviral drug recognition and elevator-type transport motions of CNT3.

Wright, N.J.Zhang, F.Suo, Y.Kong, L.Yin, Y.Fedor, J.G.Sharma, K.Borgnia, M.J.Im, W.Lee, S.Y.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01559-8
  • Primary Citation of Related Structures:  
    8TZ1, 8TZ2, 8TZ3, 8TZ4, 8TZ5, 8TZ6, 8TZ7, 8TZ8, 8TZ9, 8TZA, 8TZD

  • PubMed Abstract: 

    Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiviral drugs used in the treatment of coronavirus infections. We report high-resolution single-particle cryo-electron microscopy structures of bovine CNT3 complexed with antiviral nucleosides N 4 -hydroxycytidine, PSI-6206, GS-441524 and ribavirin, all in inward-facing states. Notably, we found that the orally bioavailable antiviral molnupiravir arrests CNT3 in four distinct conformations, allowing us to capture cryo-electron microscopy structures of drug-loaded outward-facing and drug-loaded intermediate states. Our studies uncover the conformational trajectory of CNT3 during membrane transport of a nucleoside analog antiviral drug, yield new insights into the role of interactions between the transport and the scaffold domains in elevator-like domain movements during drug translocation, and provide insights into the design of nucleoside analog antiviral prodrugs with improved oral bioavailability.


  • Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/nucleoside cotransporterA,
B [auth C],
C [auth B]
715Bos taurusMutation(s): 0 
Gene Names: SLC28A3
Membrane Entity: Yes 
UniProt
Find proteins for F1MGR1 (Bos taurus)
Explore F1MGR1 
Go to UniProtKB:  F1MGR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1MGR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBN
Query on LBN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
L [auth C]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
J [auth C]
K [auth C]
P [auth B]
D [auth A],
E [auth A],
J [auth C],
K [auth C],
P [auth B],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONcryoSPARC3.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR21AI166134

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release