6HIJ | pdb_00006hij

Cryo-EM structure of the human ABCG2-MZ29-Fab complex with cholesterol and PE lipids docked


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HIJ

This is version 2.2 of the entry. See complete history

Literature

Structural basis of small-molecule inhibition of human multidrug transporter ABCG2.

Jackson, S.M.Manolaridis, I.Kowal, J.Zechner, M.Taylor, N.M.I.Bause, M.Bauer, S.Bartholomaeus, R.Bernhardt, G.Koenig, B.Buschauer, A.Stahlberg, H.Altmann, K.H.Locher, K.P.

(2018) Nat Struct Mol Biol 25: 333-340

  • DOI: https://doi.org/10.1038/s41594-018-0049-1
  • Primary Citation Related Structures: 
    6ETI, 6FEQ, 6FFC, 6HIJ

  • PubMed Abstract: 

    ABCG2 is an ATP-binding cassette (ABC) transporter that protects tissues against xenobiotics, affects the pharmacokinetics of drugs and contributes to multidrug resistance. Although many inhibitors and modulators of ABCG2 have been developed, understanding their structure-activity relationship requires high-resolution structural insight. Here, we present cryo-EM structures of human ABCG2 bound to synthetic derivatives of the fumitremorgin C-related inhibitor Ko143 or the multidrug resistance modulator tariquidar. Both compounds are bound to the central, inward-facing cavity of ABCG2, blocking access for substrates and preventing conformational changes required for ATP hydrolysis. The high resolutions allowed for de novo building of the entire transporter and also revealed tightly bound phospholipids and cholesterol interacting with the lipid-exposed surface of the transmembrane domains (TMDs). Extensive chemical modifications of the Ko143 scaffold combined with in vitro functional analyses revealed the details of ABCG2 interactions with this compound family and provide a basis for the design of novel inhibitors and modulators.


  • Organizational Affiliation
    • Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 155.64 kDa 
  • Atom Count: 9,574 
  • Modeled Residue Count: 1,144 
  • Deposited Residue Count: 1,310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-binding cassette sub-family G member 2
A, B
655Homo sapiensMutation(s): 0 
Gene Names: ABCG2ABCPBCRPBCRP1MXR
EC: 7.6.2.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNQ0 (Homo sapiens)
Explore Q9UNQ0 
Go to UniProtKB:  Q9UNQ0
PHAROS:  Q9UNQ0
GTEx:  ENSG00000118777 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNQ0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE

Query on PEE



Download:Ideal Coordinates CCD File
C [auth A]
I [auth A]
J [auth A]
K [auth A]
R [auth B]
C [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
BWQ

Query on BWQ



Download:Ideal Coordinates CCD File
L [auth A],
V [auth B]
~{tert}-butyl 3-[(2~{S},5~{S},8~{S})-14-cyclopentyloxy-2-(2-methylpropyl)-4,7-bis(oxidanylidene)-3,6,17-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1(10),11,13,15-tetraen-5-yl]propanoate
C30 H41 N3 O5
MVNIRJAHJUCHLD-HVCNVCAESA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
SwitzerlandETH-22-14-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other
  • Version 2.0: 2025-04-09
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2025-07-02
    Changes: Data collection, Structure summary
  • Version 2.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary