5NIV | pdb_00005niv

Crystal structure of 5D3 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.205 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NIV

This is version 2.1 of the entry. See complete history

Literature

Structure of the human multidrug transporter ABCG2.

Taylor, N.M.I.Manolaridis, I.Jackson, S.M.Kowal, J.Stahlberg, H.Locher, K.P.

(2017) Nature 546: 504-509

  • DOI: https://doi.org/10.1038/nature22345
  • Primary Citation Related Structures: 
    5NIV, 5NJ3, 5NJG

  • PubMed Abstract: 

    ABCG2 is a constitutively expressed ATP-binding cassette (ABC) transporter that protects many tissues against xenobiotic molecules. Its activity affects the pharmacokinetics of commonly used drugs and limits the delivery of therapeutics into tumour cells, thus contributing to multidrug resistance. Here we present the structure of human ABCG2 determined by cryo-electron microscopy, providing the first high-resolution insight into a human multidrug transporter. We visualize ABCG2 in complex with two antigen-binding fragments of the human-specific, inhibitory antibody 5D3 that recognizes extracellular loops of the transporter. We observe two cholesterol molecules bound in the multidrug-binding pocket that is located in a central, hydrophobic, inward-facing translocation pathway between the transmembrane domains. Combined with functional in vitro analyses, our results suggest a multidrug recognition and transport mechanism of ABCG2, rationalize disease-causing single nucleotide polymorphisms and the allosteric inhibition by the 5D3 antibody, and provide the structural basis of cholesterol recognition by other G-subfamily ABC transporters.


  • Organizational Affiliation
    • Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 47.22 kDa 
  • Atom Count: 3,848 
  • Modeled Residue Count: 425 
  • Deposited Residue Count: 433 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of 5D3 Fab212Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of 5D3 Fab221Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.205 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.203α = 90
b = 45.193β = 122.14
c = 83.278γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandNCCR TransCure
ETH research grantSwitzerlandETH-22-14-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 2.0: 2024-01-17
    Changes: Atomic model, Data collection, Database references, Refinement description
  • Version 2.1: 2024-11-20
    Changes: Advisory, Structure summary