+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16069 | ||||||||||||
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Title | ABCG2 turnover-1 state with tariquidar bound | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information biotin transmembrane transporter activity / biotin transport / riboflavin transport / riboflavin transmembrane transporter activity / sphingolipid transporter activity / external side of apical plasma membrane / renal urate salt excretion / urate transmembrane transporter activity / Abacavir transmembrane transport / urate metabolic process ...biotin transmembrane transporter activity / biotin transport / riboflavin transport / riboflavin transmembrane transporter activity / sphingolipid transporter activity / external side of apical plasma membrane / renal urate salt excretion / urate transmembrane transporter activity / Abacavir transmembrane transport / urate metabolic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / organic anion transport / organic anion transmembrane transporter activity / xenobiotic transport across blood-brain barrier / transepithelial transport / export across plasma membrane / ABC-type xenobiotic transporter / Paracetamol ADME / ABC-type xenobiotic transporter activity / Ciprofloxacin ADME / NFE2L2 regulating MDR associated enzymes / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / cellular detoxification / Heme biosynthesis / Heme degradation / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / ATPase-coupled transmembrane transporter activity / Iron uptake and transport / mitochondrial membrane / brush border membrane / transmembrane transport / apical plasma membrane / membrane raft / protein homodimerization activity / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Yu Q / Kowal J / Tajkhorshid E / Locher KP | ||||||||||||
Funding support | Switzerland, United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Authors: Ali Rasouli / Qin Yu / Sepehr Dehghani-Ghahnaviyeh / Po-Chao Wen / Julia Kowal / Kaspar P Locher / Emad Tajkhorshid / Abstract: ABCG2 is an ATP-binding cassette (ABC) transporter that extrudes a wide range of xenobiotics and drugs from the cell and contributes to multidrug resistance in cancer cells. Following our recent ...ABCG2 is an ATP-binding cassette (ABC) transporter that extrudes a wide range of xenobiotics and drugs from the cell and contributes to multidrug resistance in cancer cells. Following our recent structural characterization of topotecan-bound ABCG2, here, we present cryo-EM structures of ABCG2 under turnover conditions in complex with a special modulator and slow substrate, tariquidar, in nanodiscs. The structures reveal that similar to topotecan, tariquidar induces two distinct ABCG2 conformations under turnover conditions (turnover-1 and turnover-2). μs-scale molecular dynamics simulations of drug-bound and apo ABCG2 in native-like lipid bilayers, in both topotecan- and tariquidar-bound states, characterize the ligand size as a major determinant of its binding stability. The simulations highlight direct lipid-drug interactions for the smaller topotecan, which exhibits a highly dynamic binding mode. In contrast, the larger tariquidar occupies most of the available volume in the binding pocket, thus leaving little space for lipids to enter the cavity and interact with it. Similarly, when simulating ABCG2 in the apo inward-open state, we also observe spontaneous penetration of phospholipids into the binding cavity. The captured phospholipid diffusion pathway into ABCG2 offers a putative general path to recruit any hydrophobic/amphiphilic substrates directly from the membrane. Our simulations also reveal that ABCG2 rejects cholesterol as a substrate, which is omnipresent in plasma membranes that contain ABCG2. At the same time, cholesterol is found to prohibit the penetration of phospholipids into ABCG2. These molecular findings have direct functional ramifications on ABCG2's function as a transporter. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16069.map.gz | 203.9 MB | EMDB map data format | |
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Header (meta data) | emd-16069-v30.xml emd-16069.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_16069.png | 151.2 KB | ||
Masks | emd_16069_msk_1.map | 216 MB | Mask map | |
Others | emd_16069_half_map_1.map.gz emd_16069_half_map_2.map.gz | 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16069 | HTTPS FTP |
-Validation report
Summary document | emd_16069_validation.pdf.gz | 936.5 KB | Display | EMDB validaton report |
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Full document | emd_16069_full_validation.pdf.gz | 936.1 KB | Display | |
Data in XML | emd_16069_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_16069_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16069 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16069 | HTTPS FTP |
-Related structure data
Related structure data | 8bhtMC 8bi0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16069.map.gz / Format: CCP4 / Size: 216 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: 0.66 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16069_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16069_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16069_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ABCG2 in complex with Tariquidar under turnover condition
Entire | Name: ABCG2 in complex with Tariquidar under turnover condition |
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Components |
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-Supramolecule #1: ABCG2 in complex with Tariquidar under turnover condition
Supramolecule | Name: ABCG2 in complex with Tariquidar under turnover condition type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 Details: ABCG2 was incubated with 5mM ATP, 5mM MgCl2, 0.5mM ADP, 20 uM Tariquidar at room temperature for 10 min |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 144 KDa |
-Macromolecule #1: Broad substrate specificity ATP-binding cassette transporter ABCG2
Macromolecule | Name: Broad substrate specificity ATP-binding cassette transporter ABCG2 type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type xenobiotic transporter |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73.526938 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDDDDKG SSSSNVEVFI PVSQGNTNGF PATASNDLKA FTEGAVLSFH NICYRVKLKS GFLPCRKPVE KEILSNINGI MKPGLNAIL GPTGGGKSSL LDVLAARKDP SGLSGDVLIN GAPRPANFKC NSGYVVQDDV VMGTLTVREN LQFSAALRLA T TMTNHEKN ...String: MDYKDDDDKG SSSSNVEVFI PVSQGNTNGF PATASNDLKA FTEGAVLSFH NICYRVKLKS GFLPCRKPVE KEILSNINGI MKPGLNAIL GPTGGGKSSL LDVLAARKDP SGLSGDVLIN GAPRPANFKC NSGYVVQDDV VMGTLTVREN LQFSAALRLA T TMTNHEKN ERINRVIQEL GLDKVADSKV GTQFIRGVSG GERKRTSIGM ELITDPSILF LDEPTTGLDS STANAVLLLL KR MSKQGRT IIFSIHQPRY SIFKLFDSLT LLASGRLMFH GPAQEALGYF ESAGYHCEAY NNPADFFLDI INGDSTAVAL NRE EDFKAT EIIEPSKQDK PLIEKLAEIY VNSSFYKETK AELHQLSGGE KKKKITVFKE ISYTTSFCHQ LRWVSKRSFK NLLG NPQAS IAQIIVTVVL GLVIGAIYFG LKNDSTGIQN RAGVLFFLTT NQCFSSVSAV ELFVVEKKLF IHEYISGYYR VSSYF LGKL LSDLLPMRML PSIIFTCIVY FMLGLKPKAD AFFVMMFTLM MVAYSASSMA LAIAAGQSVV SVATLLMTIC FVFMMI FSG LLVNLTTIAS WLSWLQYFSI PRYGFTALQH NEFLGQNFCP GLNATGNNPC NYATCTGEEY LVKQGIDLSP WGLWKNH VA LACMIVIFLT IAYLKLLFLK KYS |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #3: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #4: tariquidar
Macromolecule | Name: tariquidar / type: ligand / ID: 4 / Number of copies: 1 / Formula: R1H |
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Molecular weight | Theoretical: 646.732 Da |
Chemical component information | ChemComp-R1H: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | This sample was mono-disperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.49 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Target criteria: cross-correlation coefficient |
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Output model | PDB-8bht: |