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- EMDB-25442: Cryo-EM structure of prestin from gerbil (Meriones unguiculatus) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-25442
TitleCryo-EM structure of prestin from gerbil (Meriones unguiculatus) in the presence of NaCl
Map data
Sample
  • Complex: Prestin dimer surrounded by a belt of detergent
    • Protein or peptide: Prestin, Enhanced Yellow Fluorescent Protein chimera
KeywordsPrestin (Slc26a5) / cochlear amplification / NonLinear Capacitance / MEMBRANE PROTEIN / MOTOR PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsButan C / Santos-Sacchi J
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sun
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25442.png

Downloads & links

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Map

FileDownload / File: emd_25442.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.068 Å
Density
Contour LevelBy AUTHOR: 0.0233 / Movie #1: 0.0233
Minimum - Maximum-0.06466008 - 0.14309588
Average (Standard dev.)0.00019112107 (±0.0051936614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.31998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0681.0681.068
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z256.320256.320256.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0650.1430.000

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Supplemental data

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Sample components

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Entire : Prestin dimer surrounded by a belt of detergent

EntireName: Prestin dimer surrounded by a belt of detergent
Components
  • Complex: Prestin dimer surrounded by a belt of detergent
    • Protein or peptide: Prestin, Enhanced Yellow Fluorescent Protein chimera

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Supramolecule #1: Prestin dimer surrounded by a belt of detergent

SupramoleculeName: Prestin dimer surrounded by a belt of detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Meriones unguiculatus (Mongolian gerbil)

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Macromolecule #1: Prestin, Enhanced Yellow Fluorescent Protein chimera

MacromoleculeName: Prestin, Enhanced Yellow Fluorescent Protein chimera / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 111.865805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDHAEENEIP VATQKYHVER PIFSHPVLQE RLHVKDKVSE SIGDKLKQAF TCTPKKIRNI IYMFLPITKW LPAYKFKEYV LGDLVSGIS TGVLQLPQGL AFAMLAAVPP VFGLYSSFYP VIMYCFFGTS RHISIGPFAV ISLMIGGVAV RLVPDDIVIP G GVNATNGT ...String:
MDHAEENEIP VATQKYHVER PIFSHPVLQE RLHVKDKVSE SIGDKLKQAF TCTPKKIRNI IYMFLPITKW LPAYKFKEYV LGDLVSGIS TGVLQLPQGL AFAMLAAVPP VFGLYSSFYP VIMYCFFGTS RHISIGPFAV ISLMIGGVAV RLVPDDIVIP G GVNATNGT EARDALRVKV AMSVTLLSGI IQFCLGVCRF GFVAIYLTEP LVRGFTTAAA VHVFTSMLKY LFGVKTKRYS GI FSVVYST VAVLQNVKNL NVCSLGVGLM VFGLLLGGKE FNERFKEKLP APIPLEFFAV VMGTGISAGF NLHESYSVDV VGT LPLGLL PPANPDTSLF HLVYVDAIAI AIVGFSVTIS MAKTLANKHG YQVDGNQELI ALGICNSIGS LFQTFSISCS LSRS LVQEG TGGKTQLAGC LASLMILLVI LATGFLFESL PQAVLSAIVI VNLKGMFMQF SDLPFFWRTS KIELTIWLTT FVSSL FLGL DYGLITAVII ALLTVIYRTQ SPSYKVLGQL PDTDVYIDID AYEEVKEIPG IKIFQINAPI YYANSDLYSN ALKRKT GVN PALIMGARRK AMRKYAKEVG NANIANAAVV KVDGEVDGEN ATKPEEEDDE VKYPPIVIKT TFPEELQRFM PQTENVH TI ILDFTQVNFI DSVGVKTLAV MVKEYGDVGI YVYLAGCSPQ VVNDLTRNRF FENPALKELL FHSIHDAVLG SHVREAMA E QEASAPPPQD DMEPNATPTT PEAARDPPVA TMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFI CTTGKLPVPW PTLVTTFGYG LQCFARYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNI LGHKLEYNYN SHNVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSYQSA L SKDPNEKR DHMVLLEFVT AAGITLGMDE LYKEQKLISE EDLNMHTGHH HHHH

UniProtKB: Prestin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 10 mM HEPES, 200 mM NaCl, 0.02% GDN, pH 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.15 µm / Nominal defocus min: 1.1500000000000001 µm / Nominal magnification: 81000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rtf

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 111863
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6rtf


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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