Structure of CNTnw in an inward-facing substrate-bound state

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Visualizing multistep elevator-like transitions of a nucleoside transporter.

Hirschi, M.Johnson, Z.L.Lee, S.Y.

(2017) Nature 545: 66-70

  • DOI: https://doi.org/10.1038/nature22057
  • Primary Citation of Related Structures:  
    5L24, 5L26, 5L27, 5L2A, 5L2B, 5U9W

  • PubMed Abstract: 

    Membrane transporters move substrates across the membrane by alternating access of their binding sites between the opposite sides of the membrane. An emerging model of this process is the elevator mechanism, in which a substrate-binding transport domain moves a large distance across the membrane. This mechanism has been characterized by a transition between two states, but the conformational path that leads to the transition is not yet known, largely because the available structural information has been limited to the two end states. Here we present crystal structures of the inward-facing, intermediate, and outward-facing states of a concentrative nucleoside transporter from Neisseria wadsworthii. Notably, we determined the structures of multiple intermediate conformations, in which the transport domain is captured halfway through its elevator motion. Our structures present a trajectory of the conformational transition in the elevator model, revealing multiple intermediate steps and state-dependent conformational changes within the transport domain that are associated with the elevator-like motion.

  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, North Carolina 27710, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside permease
A, B, C
431Neisseria wadsworthii 9715Mutation(s): 0 
Gene Names: nupCHMPREF9370_1765
Membrane Entity: Yes 
Find proteins for G4CRQ5 (Neisseria wadsworthii 9715)
Explore G4CRQ5 
Go to UniProtKB:  G4CRQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4CRQ5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6ZL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
O [auth C],
P [auth C]
2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-2-octyldecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
C43 H80 O22
Query on URI

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
Q [auth C]
C9 H12 N2 O6
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
R [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.22α = 90
b = 115.22β = 90
c = 264.028γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2017-05-10
    Changes: Database references
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description