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Yorodumi- EMDB-20945: Cryo-EM structure of wild-type bovine multidrug resistance protei... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20945 | |||||||||
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Title | Cryo-EM structure of wild-type bovine multidrug resistance protein 1 (MRP1) under active turnover conditions | |||||||||
Map data | 3.23-Angstrom cryo-EM reconstruction of wild-type bovine MRP1 under active turnover conditions in the presence of ATP and leukotriene C4 | |||||||||
Sample |
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Keywords | ABC transporter / multidrug resistance / outward facing / TRANSPORT PROTEIN / MRP1 | |||||||||
Function / homology | Function and homology information Sphingolipid de novo biosynthesis / Heme degradation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / cyclic nucleotide transport / Transport of RCbl within the body / Paracetamol ADME / leukotriene transport / glutathione transmembrane transport / glutathione transmembrane transporter activity / ABC-type glutathione-S-conjugate transporter ...Sphingolipid de novo biosynthesis / Heme degradation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / cyclic nucleotide transport / Transport of RCbl within the body / Paracetamol ADME / leukotriene transport / glutathione transmembrane transport / glutathione transmembrane transporter activity / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / ABC-family proteins mediated transport / Cytoprotection by HMOX1 / ABC-type xenobiotic transporter / xenobiotic transport / ABC-type xenobiotic transporter activity / lipid transport / xenobiotic transmembrane transporter activity / ABC-type transporter activity / positive regulation of inflammatory response / basolateral plasma membrane / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Johnson ZL / Chen J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2020 Title: Characterization of the kinetic cycle of an ABC transporter by single-molecule and cryo-EM analyses. Authors: Ling Wang / Zachary Lee Johnson / Michael R Wasserman / Jesper Levring / Jue Chen / Shixin Liu / Abstract: ATP-binding cassette (ABC) transporters are molecular pumps ubiquitous across all kingdoms of life. While their structures have been widely reported, the kinetics governing their transport cycles ...ATP-binding cassette (ABC) transporters are molecular pumps ubiquitous across all kingdoms of life. While their structures have been widely reported, the kinetics governing their transport cycles remain largely unexplored. Multidrug resistance protein 1 (MRP1) is an ABC exporter that extrudes a variety of chemotherapeutic agents and native substrates. Previously, the structures of MRP1 were determined in an inward-facing (IF) or outward-facing (OF) conformation. Here, we used single-molecule fluorescence spectroscopy to track the conformational changes of bovine MRP1 (bMRP1) in real time. We also determined the structure of bMRP1 under active turnover conditions. Our results show that substrate stimulates ATP hydrolysis by accelerating the IF-to-OF transition. The rate-limiting step of the transport cycle is the dissociation of the nucleotide-binding-domain dimer, while ATP hydrolysis per se does not reset MRP1 to the resting state. The combination of structural and kinetic data illustrates how different conformations of MRP1 are temporally linked and how substrate and ATP alter protein dynamics to achieve active transport. | |||||||||
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_20945.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-20945-v30.xml emd-20945.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20945_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_20945.png | 126.2 KB | ||
Filedesc metadata | emd-20945.cif.gz | 7.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20945 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20945 | HTTPS FTP |
-Validation report
Summary document | emd_20945_validation.pdf.gz | 583.1 KB | Display | EMDB validaton report |
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Full document | emd_20945_full_validation.pdf.gz | 582.7 KB | Display | |
Data in XML | emd_20945_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_20945_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20945 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20945 | HTTPS FTP |
-Related structure data
Related structure data | 6uy0MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20945.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3.23-Angstrom cryo-EM reconstruction of wild-type bovine MRP1 under active turnover conditions in the presence of ATP and leukotriene C4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 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 : bovine multidrug resistance protein 1 (MRP1)
Entire | Name: bovine multidrug resistance protein 1 (MRP1) |
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Components |
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-Supramolecule #1: bovine multidrug resistance protein 1 (MRP1)
Supramolecule | Name: bovine multidrug resistance protein 1 (MRP1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 170 KDa |
-Macromolecule #1: Multidrug resistance-associated protein 1
Macromolecule | Name: Multidrug resistance-associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type xenobiotic transporter |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 172.862562 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MALRDFCSVD GSDLFWEWNV TWNTSNPDFT KCFQNTVLVW VPCSYLWVCF PFYFLYLSHH DRGYIQMTHL NKAKTALGFL LWIVCWADL FYSFWERSMG KLLAPVFLVS PTLLGITMLL ATFLIQIERR RGVQSSGIML TFWLIALLCA LAILRSKIMT A LKEDARVD ...String: MALRDFCSVD GSDLFWEWNV TWNTSNPDFT KCFQNTVLVW VPCSYLWVCF PFYFLYLSHH DRGYIQMTHL NKAKTALGFL LWIVCWADL FYSFWERSMG KLLAPVFLVS PTLLGITMLL ATFLIQIERR RGVQSSGIML TFWLIALLCA LAILRSKIMT A LKEDARVD VFRDVTFYIY FSLVLIQLVL SCFSDRSPLF SETINDPNPC PESSASFLSR ITFWWITGMM VQGYRQPLES TD LWSLNKE DTSEQVVPVL VKNWKKECAK SRKQPVKIVY SSKDPAKPKG SSKVDVNEEA EALIVKCPQK ERDPSLFKVL YKT FGPYFL MSFLFKAVHD LMMFAGPEIL KLLINFVNDK KAPEWQGYFY TALLFISACL QTLVLHQYFH ICFVSGMRIK TAVI GAVYR KALVITNAAR KSSTVGEIVN LMSVDAQRFM DLATYINMIW SAPLQVILAL YLLWLNLGPS VLAGVAVMVL MVPLN AVMA MKTKTYQVAH MKSKDNRIKL MNEILNGIKV LKLYAWELAF KDKVLAIRQE ELKVLKKSAY LAAVGTFTWV CTPFLV ALS TFAVYVTVDE NNILDAQKAF VSLALFNILR FPLNILPMVI SSIVQASVSL KRLRVFLSHE DLDPDSIQRR PIKDAGA TN SITVKNATFT WARNDPPTLH GITFSVPEGS LVAVVGQVGC GKSSLLSALL AEMDKVEGHV TVKGSVAYVP QQAWIQNI S LRENILFGRQ LQERYYKAVV EACALLPDLE ILPSGDRTEI GEKGVNLSGG QKQRVSLARA VYCDSDVYLL DDPLSAVDA HVGKHIFENV IGPKGLLKNK TRLLVTHAIS YLPQMDVIIV MSGGKISEMG SYQELLARDG AFAEFLRTYA SAEQEQGQPE DGLAGVGGP GKEVKQMENG MLVTDTAGKQ MQRQLSSSSS YSRDVSQHHT STAELRKPGP TEETWKLVEA DKAQTGQVKL S VYWDYMKA IGLFISFLSI FLFLCNHVAS LVSNYWLSLW TDDPIVNGTQ EHTQVRLSVY GALGISQGIT VFGYSMAVSI GG IFASRRL HLDLLHNVLR SPISFFERTP SGNLVNRFSK ELDTVDSMIP QVIKMFMGSL FNVIGACIII LLATPMAAVI IPP LGLIYF FVQRFYVASS RQLKRLESVS RSPVYSHFNE TLLGVSVIRA FEEQERFIRQ SDLKVDENQK AYYPSIVANR WLAV RLECV GNCIVLFASL FAVISRHSLS AGLVGLSVSY SLQVTTYLNW LVRMSSEMET NIVAVERLKE YSETEKEAPW QIQDM APPK DWPQVGRVEF RDYGLRYRED LDLVLKHINV TIDGGEKVGI VGRTGAGKSS LTLGLFRIKE SAEGEIIIDD INIAKI GLH DLRFKITIIP QDPVLFSGSL RMNLDPFSQY SDEEVWTSLE LAHLKGFVSA LPDKLNHECA EGGENLSVGQ RQLVCLA RA LLRKTKILVL DEATAAVDLE TDDLIQSTIR TQFDDCTVLT IAHRLNTIMD YTRVIVLDKG EIQEWGSPSD LLQQRGLF Y SMAKDSGLVS NSLEVLFQ UniProtKB: Multidrug resistance-associated protein 1 |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 3 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.3 mg/mL | ||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 100.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 3993 / Average exposure time: 10.0 sec. / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |