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- PDB-7s9d: Cryo-EM Structure of dolphin Prestin: Intermediate state -

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Basic information

Entry
Database: PDB / ID: 7s9d
TitleCryo-EM Structure of dolphin Prestin: Intermediate state
ComponentsPrestin
KeywordsMOTOR PROTEIN / Outer hair cells / electromotility / mechanotransduction / hearing / deafness / frequency sensation / echolocation / SLC26 / SLC26A5
Function / homology
Function and homology information


cochlear outer hair cell electromotile response / oxalate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / sensory perception of sound / regulation of cell shape / plasma membrane
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
Biological speciesTursiops truncatus (common bottlenose dolphin)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsBavi, N. / Clark, M.D. / Contreras, G.F. / Shen, R. / Reddy, B.G. / Milewski, W. / Perozo, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC019833 United States
CitationJournal: 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
DepositionSep 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Prestin
B: Prestin


Theoretical massNumber of molelcules
Total (without water)161,9482
Polymers161,9482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Prestin / Solute carrier family 26 member 5


Mass: 80973.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tursiops truncatus (common bottlenose dolphin)
Gene: SLC26A5 / Production host: Homo sapiens (human) / References: UniProt: D7PC76

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dolphin Prestin: Intermediate state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Tursiops truncatus (common bottlenose dolphin)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Hek 293
Buffer solutionpH: 7.4
Details: 125 mM Na2SO4, 5mM Mg(OH)2, 20 mM Tris-OH, 10-15 mM methanesulfonic acid + 0.02 % GDN
Buffer componentConc.: 125 mM / Name: sodium Sulfate / Formula: Na2SO4
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Monodisperse peak at around 14 ml using SEC (Superose 6 column)
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: 4.5 s blot times, blot force 3, and double filter papers on each side of the vitrobot.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92000 / Symmetry type: POINT

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