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- PDB-7sun: Atomic model of prestin from gerbil (Meriones unguiculatus) -

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Basic information

Entry
Database: PDB / ID: 7sun
TitleAtomic model of prestin from gerbil (Meriones unguiculatus)
ComponentsPrestin, Enhanced Yellow Fluorescent Protein chimera
KeywordsMEMBRANE PROTEIN / MOTOR PROTEIN / Prestin (Slc26a5) / cochlear amplification / NonLinear Capacitance
Function / homology
Function and homology information


secondary active sulfate transmembrane transporter activity / sensory perception of sound / regulation of cell shape / basolateral plasma membrane / membrane => GO:0016020
Similarity search - Function
Prestin / 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 speciesMeriones unguiculatus (Mongolian gerbil)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsButan, C. / Santos-Sacchi, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC016318, R01 DC008130 United States
CitationJournal: Nat Commun / Year: 2022
Title: Single particle cryo-EM structure of the outer hair cell motor protein prestin.
Authors: Carmen Butan / Qiang Song / Jun-Ping Bai / Winston J T Tan / Dhasakumar Navaratnam / Joseph Santos-Sacchi /
Abstract: The mammalian outer hair cell (OHC) protein prestin (Slc26a5) differs from other Slc26 family members due to its unique piezoelectric-like property that drives OHC electromotility, the putative ...The mammalian outer hair cell (OHC) protein prestin (Slc26a5) differs from other Slc26 family members due to its unique piezoelectric-like property that drives OHC electromotility, the putative mechanism for cochlear amplification. Here, we use cryo-electron microscopy to determine prestin's structure at 3.6 Å resolution. Prestin is structurally similar to the anion transporter Slc26a9. It is captured in an inward-open state which may reflect prestin's contracted state. Two well-separated transmembrane (TM) domains and two cytoplasmic sulfate transporter and anti-sigma factor antagonist (STAS) domains form a swapped dimer. The transmembrane domains consist of 14 transmembrane segments organized in two 7+7 inverted repeats, an architecture first observed in the bacterial symporter UraA. Mutation of prestin's chloride binding site removes salicylate competition with anions while retaining the prestin characteristic displacement currents (Nonlinear Capacitance), undermining the extrinsic voltage sensor hypothesis for prestin function.
History
DepositionNov 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Prestin, Enhanced Yellow Fluorescent Protein chimera
B: Prestin, Enhanced Yellow Fluorescent Protein chimera


Theoretical massNumber of molelcules
Total (without water)223,7322
Polymers223,7322
Non-polymers00
Water0
1


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

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Components

#1: Protein Prestin, Enhanced Yellow Fluorescent Protein chimera / / Solute carrier family 26 member 5


Mass: 111865.805 Da / Num. of mol.: 2 / Fragment: prestin + linker + eYFP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meriones unguiculatus (Mongolian gerbil), (gene. exp.) synthetic construct (others)
Gene: SLC26A5, PRES, eYFP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9JKQ2

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Prestin dimer surrounded by a belt of detergent / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Meriones unguiculatus (Mongolian gerbil)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4 / Details: 10 mM HEPES, 200 mM NaCl, 0.02% GDN, pH 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2150 nm / Nominal defocus min: 1150 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4_1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111863 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6RTF

6rtf


Accession code: 6RTF / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310686
ELECTRON MICROSCOPYf_angle_d0.6814516
ELECTRON MICROSCOPYf_dihedral_angle_d4.3251442
ELECTRON MICROSCOPYf_chiral_restr0.0461728
ELECTRON MICROSCOPYf_plane_restr0.0051804

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