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Yorodumi- EMDB-24934: Cryo-EM Structure of dolphin Prestin: Inhibited II (Sulfate +Sali... -
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-Basic information
Entry | Database: EMDB / ID: EMD-24934 | |||||||||
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Title | Cryo-EM Structure of dolphin Prestin: Inhibited II (Sulfate +Salicylate) state | |||||||||
Map data | Sulfate Salicylate | |||||||||
Sample |
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Keywords | Outer hair cells / electromotility / mechanotransduction / hearing / deafness / frequency sensation / echolocation / SLC26 / SLC26A5 / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information cochlear outer hair cell electromotile response / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / sensory perception of sound / regulation of cell shape / plasma membrane Similarity search - Function | |||||||||
Biological species | Tursiops truncatus (common bottlenose dolphin) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Bavi N / Clark MD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2021 Title: The conformational cycle of prestin underlies outer-hair cell electromotility. Authors: Navid Bavi / Michael David Clark / Gustavo F Contreras / Rong Shen / Bharat G Reddy / Wieslawa Milewski / Eduardo Perozo / Abstract: The voltage-dependent motor protein prestin (also known as SLC26A5) is responsible for the electromotive behaviour of outer-hair cells and underlies the cochlear amplifier. Knockout or impairment of ...The voltage-dependent motor protein prestin (also known as SLC26A5) is responsible for the electromotive behaviour of outer-hair cells and underlies the cochlear amplifier. Knockout or impairment of prestin causes severe hearing loss. Despite the key role of prestin in hearing, the mechanism by which mammalian prestin senses voltage and transduces it into cellular-scale movements (electromotility) is poorly understood. Here we determined the structure of dolphin prestin in six distinct states using single-particle cryo-electron microscopy. Our structural and functional data suggest that prestin adopts a unique and complex set of states, tunable by the identity of bound anions (Cl or SO). Salicylate, a drug that can cause reversible hearing loss, competes for the anion-binding site of prestin, and inhibits its function by immobilizing prestin in a new conformation. Our data suggest that the bound anion together with its coordinating charged residues and helical dipole act as a dynamic voltage sensor. An analysis of all of the anion-dependent conformations reveals how structural rearrangements in the voltage sensor are coupled to conformational transitions at the protein-membrane interface, suggesting a previously undescribed mechanism of area expansion. Visualization of the electromotility cycle of prestin distinguishes the protein from the closely related SLC26 anion transporters, highlighting the basis for evolutionary specialization of the mammalian cochlear amplifier at a high resolution. | |||||||||
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_24934.map.gz | 52.2 MB | EMDB map data format | |
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Header (meta data) | emd-24934-v30.xml emd-24934.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24934_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_24934.png | 94.1 KB | ||
Filedesc metadata | emd-24934.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24934 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24934 | HTTPS FTP |
-Validation report
Summary document | emd_24934_validation.pdf.gz | 593.1 KB | Display | EMDB validaton report |
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Full document | emd_24934_full_validation.pdf.gz | 592.7 KB | Display | |
Data in XML | emd_24934_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_24934_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24934 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24934 | HTTPS FTP |
-Related structure data
Related structure data | 7s9eMC 7s8xC 7s9aC 7s9bC 7s9cC 7s9dC 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_24934.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sulfate Salicylate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 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 : Cryo-EM Structure of dolphin Prestin in complex with Salicylate: ...
Entire | Name: Cryo-EM Structure of dolphin Prestin in complex with Salicylate: Inhibited II, Sulfate + Salicylate |
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Components |
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-Supramolecule #1: Cryo-EM Structure of dolphin Prestin in complex with Salicylate: ...
Supramolecule | Name: Cryo-EM Structure of dolphin Prestin in complex with Salicylate: Inhibited II, Sulfate + Salicylate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Tursiops truncatus (common bottlenose dolphin) |
-Macromolecule #1: Prestin
Macromolecule | Name: Prestin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Tursiops truncatus (common bottlenose dolphin) |
Molecular weight | Theoretical: 80.97375 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDHVEETEIL AATQRYYVER PIFSHPVLQE RLHKKDKISE SIGDKLKQAF TCTPKKIRNI IYMFLPITKW LPAYRFKEYV LGDIVSGIS TGVLQLPQGL AFAMLAAVPP VFGLYSSFYP VIMYCFFGTS RHISIGPFAV ISLMIGGVAV RLVPDDIVIP G GVNATNST ...String: MDHVEETEIL AATQRYYVER PIFSHPVLQE RLHKKDKISE SIGDKLKQAF TCTPKKIRNI IYMFLPITKW LPAYRFKEYV LGDIVSGIS TGVLQLPQGL AFAMLAAVPP VFGLYSSFYP VIMYCFFGTS RHISIGPFAV ISLMIGGVAV RLVPDDIVIP G GVNATNST EARDALRVKV AMSVTLLTGI IQFCLGVCRF GFVAIYLTEP LVRGFTTAAA VHVFTSMLKY LFGVKTKRYS GI FSVVYST VAVLQNVKNL NVCSLGVGLM VFGLLLGGKE FNERFKEKLP APIPLEFFAV VMGTGISAGF SLHESYNVDV VGT LPLGLL PPANPDTSLF HLVYVDAIAI AIVGFSVTIS MAKTLANKHG YQVDGNQELI ALGLCNSTGS LFQTFAISCS LSRS LVQEG TGGKTQLAGC LASLMILLVI LATGFLFESL PQAVLSAIVI VNLKGMFMQF SDLPFFWRTS KIELTIWLTT FVSSL FLGL DYGLITAVII ALMTVIYRTQ SPSYIVLGQL PDTDVYIDID AYEEVKEVPG IKIFQINAPI YYANSDLYSS ALKRKT GVN PAFILGARRK AMKKYAKEVG NANMANATVV KVDAEVDAED GTKPEEEEDE IKYPPIVTKS TLPEELQRFM PPGDNVH TI ILDFTQVNFM DSVGVKTLAG IVKEYGDVGI YVYLAGCSAQ VVSDLTQNQF FENPALLDLL FHSIHDAVLG SQVREALA E QEATAAPPQE DSEPNATPEA UniProtKB: Prestin |
-Macromolecule #2: 2-HYDROXYBENZOIC ACID
Macromolecule | Name: 2-HYDROXYBENZOIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: SAL |
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Molecular weight | Theoretical: 138.121 Da |
Chemical component information | ChemComp-SAL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 125.0 mM / Component - Formula: Na2SO4 / Component - Name: sodium sulfate Details: 125 mM Na2SO4, 5mM Mg(OH)2, 20 mM Tris-OH, 10-15 mM methanesulfonic acid + 0.02 % GDN + 50 mM Sodium Salicylate |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: 4.5 s blot times, blot force 3, and double filter papers on each side of the vitrobot.. |
Details | Monodisperse peak at around 14 ml using SEC (Superose 6 column) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 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 |