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Yorodumi- EMDB-4284: Apo form of UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4284 | |||||||||
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Title | Apo form of UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1HM). Map3 (straight conformation of TM4 and TM10) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.55 Å | |||||||||
Authors | Alam A / Locher KP | |||||||||
Citation | Journal: 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4284.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-4284-v30.xml emd-4284.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_4284.png | 114.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4284 | HTTPS FTP |
-Validation report
Summary document | emd_4284_validation.pdf.gz | 273.4 KB | Display | EMDB validaton report |
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Full document | emd_4284_full_validation.pdf.gz | 272.6 KB | Display | |
Data in XML | emd_4284_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4284 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4284 | HTTPS FTP |
-Related structure data
Related structure data | 4281C 4282C 4283C 4285C 6fn1C 6fn4C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4284.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.387 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Apo Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab
Entire | Name: Apo Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab |
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Components |
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-Supramolecule #1: Apo Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab
Supramolecule | Name: Apo Human-mouse chimeric ABCB1 (ABCB1HM) complex with UIC2 fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 195 KDa |
-Supramolecule #2: Apo Human-mouse chimeric ABCB1 (ABCB1HM)
Supramolecule | Name: Apo Human-mouse chimeric ABCB1 (ABCB1HM) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 142 KDa |
-Supramolecule #3: UIC2 fab
Supramolecule | Name: UIC2 fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 48.7 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 0.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158827 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |