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- EMDB-4281: Zosuquidar and UIC2 Fab complex of human-mouse chimeric ABCB1 (AB... -

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Basic information

Entry
Database: EMDB / ID: 4281
TitleZosuquidar and UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1HM)
Map dataZosuquidar complex of ABCB1HM-X. Final post-processed map after partial detergent belt removal.
SampleHuman-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab and zosuquidar
  • Human-mouse chimeric ABCB1 (ABCBHM)
  • (UIC2 Antigen Binding Fragment ...) x 2
  • (ligand) x 2
Function / homologyType I protein exporter / ABC transporter-like / ABC-family proteins mediated transport / Abacavir transmembrane transport / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / ABC transporter / ABC transporter type 1, transmembrane domain superfamily ...Type I protein exporter / ABC transporter-like / ABC-family proteins mediated transport / Abacavir transmembrane transport / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / ABC transporter / ABC transporter type 1, transmembrane domain superfamily / Multidrug resistance protein 1 / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain / AAA+ ATPase domain / ceramide translocation / ceramide-translocating ATPase activity / positive regulation of anion channel activity / phosphatidylethanolamine-translocating ATPase activity / ec:7.6.2.2: / phosphatidylcholine-translocating ATPase activity / regulation of response to osmotic stress / phospholipid translocation / xenobiotic transmembrane transporting ATPase activity / stem cell proliferation / ATPase activity, coupled to transmembrane movement of substances / transporter activity / regulation of chloride transport / transmembrane transport / apical plasma membrane / G2/M transition of mitotic cell cycle / response to drug / cell surface / extracellular exosome / membrane / integral component of membrane / ATP binding / plasma membrane / Multidrug resistance protein 1
Function and homology information
SourceHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3.58 Å resolution
AuthorsAlam A / Locher KP
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of a zosuquidar and UIC2-bound human-mouse chimeric ABCB1.
Authors: Amer Alam / Raphael Küng / Julia Kowal / Robert A McLeod / Nina Tremp / Eugenia V Broude / Igor B Roninson / Henning Stahlberg / Kaspar P Locher
Abstract: The multidrug transporter ABCB1 (P-glycoprotein) is an ATP-binding cassette transporter that has a key role in protecting tissues from toxic insult and contributes to multidrug extrusion from cancer ...The multidrug transporter ABCB1 (P-glycoprotein) is an ATP-binding cassette transporter that has a key role in protecting tissues from toxic insult and contributes to multidrug extrusion from cancer cells. Here, we report the near-atomic resolution cryo-EM structure of nucleotide-free ABCB1 trapped by an engineered disulfide cross-link between the nucleotide-binding domains (NBDs) and bound to the antigen-binding fragment of the human-specific inhibitory antibody UIC2 and to the third-generation ABCB1 inhibitor zosuquidar. Our structure reveals the transporter in an occluded conformation with a central, enclosed, inhibitor-binding pocket lined by residues from all transmembrane (TM) helices of ABCB1. The pocket spans almost the entire width of the lipid membrane and is occupied exclusively by two closely interacting zosuquidar molecules. The external, conformational epitope facilitating UIC2 binding is also visualized, providing a basis for its inhibition of substrate efflux. Additional cryo-EM structures suggest concerted movement of TM helices from both halves of the transporters associated with closing the NBD gap, as well as zosuquidar binding. Our results define distinct recognition interfaces of ABCB1 inhibitory agents, which may be exploited for therapeutic purposes.
Validation ReportPDB-ID: 6fn1

SummaryFull reportAbout validation report
DateDeposition: Feb 2, 2018 / Header (metadata) release: Feb 21, 2018 / Map release: Feb 21, 2018 / Last update: Mar 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6fn1
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4281.map.gz (map file in CCP4 format, 171501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
350 pix
0.84 Å/pix.
= 294. Å
350 pix
0.84 Å/pix.
= 294. Å
350 pix
0.84 Å/pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.13838151 - 0.22620861
Average (Standard dev.)-0.000044547967 (0.004538118)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions350350350
Origin0.00.00.0
Limit349.0349.0349.0
Spacing350350350
CellA=B=C: 294.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.1380.226-0.000

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Supplemental data

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Sample components

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Entire Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab and zo...

EntireName: Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab and zosuquidar
Number of components: 8

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Component #1: protein, Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 f...

ProteinName: Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab and zosuquidar
Recombinant expression: No
MassTheoretical: 195 kDa

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Component #2: protein, Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 f...

ProteinName: Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab and zosuquidar
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 f...

ProteinName: Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab and zosuquidar
Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #4: protein, Human-mouse chimeric ABCB1 (ABCBHM)

ProteinName: Human-mouse chimeric ABCB1 (ABCBHM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.719953 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, UIC2 Antigen Binding Fragment Light chain

ProteinName: UIC2 Antigen Binding Fragment Light chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.321039 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #6: protein, UIC2 Antigen Binding Fragment Heavy Chain

ProteinName: UIC2 Antigen Binding Fragment Heavy Chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.381281 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #8: ligand, Zosuquidar

LigandName: Zosuquidar / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.527604 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.54 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 231969
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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