8PY4

ABCG2 in complex with ko143 and 5D3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Modulation of ABCG2 Transporter Activity by Ko143 Derivatives.

Yu, Q.Dehghani-Ghahnaviyeh, S.Rasouli, A.Sadurni, A.Kowal, J.Bang-Soerensen, R.Wen, P.C.Tinzl-Zechner, M.Irobalieva, R.N.Ni, D.Stahlberg, H.Altmann, K.H.Tajkhorshid, E.Locher, K.P.

(2024) ACS Chem Biol 

  • DOI: https://doi.org/10.1021/acschembio.4c00353
  • Primary Citation of Related Structures:  
    8PXO, 8PY4, 8Q7B, 8QCM

  • PubMed Abstract: 

    ABCG2 is a multidrug transporter that protects tissues from xenobiotics, affects drug pharmacokinetics, and contributes to multidrug resistance of cancer cells. Here, we present tetracyclic fumitremorgin C analog Ko143 derivatives, evaluate their in vitro modulation of purified ABCG2, and report four high-resolution cryo-EM structures and computational analyses to elucidate their interactions with ABCG2. We found that Ko143 derivatives that are based on a ring-opened scaffold no longer inhibit ABCG2-mediated transport activity. In contrast, closed-ring, tetracyclic analogs were highly potent inhibitors. Strikingly, the least potent of these compounds, MZ82, bound deeper into the central ABCG2 cavity than the other inhibitors and it led to partial closure of the transmembrane domains and increased flexibility of the nucleotide-binding domains. Minor structural modifications can thus convert a potent inhibitor into a compound that induces conformational changes in ABCG2 similar to those observed during binding of a substrate. Molecular dynamics simulations and free energy binding calculations further supported the correlation between reduced potency and distinct binding pose of the compounds. We introduce the highly potent inhibitor AZ99 that may exhibit improved in vivo stability.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich 8093, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5d3(fab) heavy chain variable domainA [auth D],
C [auth F]
221Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
5D3(Fab) light chain variable domainB [auth E],
F [auth C]
214Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Broad substrate specificity ATP-binding cassette transporter ABCG2D [auth B],
E [auth A]
665Homo sapiensMutation(s): 0 
Gene Names: ABCG2ABCPBCRPBCRP1MXR
EC: 7.6.2.2
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9UNQ0-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
2N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3O (Subject of Investigation/LOI)
Query on I3O

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A]
tert-butyl 3-[(2S,5S,8S)-14-methoxy-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
C26 H35 N3 O5
NXNRAECHCJZNRF-JBACZVJFSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
M [auth B]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release