6QEX

Nanodisc reconstituted human ABCB1 in complex with UIC2 fab and taxol


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insight into substrate and inhibitor discrimination by human P-glycoprotein.

Alam, A.Kowal, J.Broude, E.Roninson, I.Locher, K.P.

(2019) Science 363: 753-756

  • DOI: https://doi.org/10.1126/science.aav7102
  • Primary Citation of Related Structures:  
    6QEE, 6QEX

  • PubMed Abstract: 

    ABCB1, also known as P-glycoprotein, actively extrudes xenobiotic compounds across the plasma membrane of diverse cells, which contributes to cellular drug resistance and interferes with therapeutic drug delivery. We determined the 3.5-angstrom cryo-electron microscopy structure of substrate-bound human ABCB1 reconstituted in lipidic nanodiscs, revealing a single molecule of the chemotherapeutic compound paclitaxel (Taxol) bound in a central, occluded pocket. A second structure of inhibited, human-mouse chimeric ABCB1 revealed two molecules of zosuquidar occupying the same drug-binding pocket. Minor structural differences between substrate- and inhibitor-bound ABCB1 sites are amplified toward the nucleotide-binding domains (NBDs), revealing how the plasticity of the drug-binding site controls the dynamics of the adenosine triphosphate-hydrolyzing NBDs. Ordered cholesterol and phospholipid molecules suggest how the membrane modulates the conformational changes associated with drug binding and transport.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug resistance protein 11,280Homo sapiensMutation(s): 1 
Gene Names: ABCB1MDR1PGY1
EC: 7.6.2.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08183 (Homo sapiens)
Explore P08183 
Go to UniProtKB:  P08183
GTEx:  ENSG00000085563 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08183
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UIC2 Fab lightchain220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UIC2 Fab heavy chain225Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download Ideal Coordinates CCD File 
W [auth A]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
X [auth A],
Y [auth A]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TA1 BindingDB:  6QEX IC50: min: 2596, max: 3.27e+5 (nM) from 6 assay(s)
CLR BindingDB:  6QEX IC50: 8200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
European Molecular Biology OrganizationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Other
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-06-02
    Changes: Structure summary