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- EMDB-23334: Structure of human prestin in the presence of sodium salicylate a... -

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Basic information

Entry
Database: EMDB / ID: EMD-23334
TitleStructure of human prestin in the presence of sodium salicylate and sodium sulfate
Map dataPrestin in the presence of sodium salicylate and sodium sulfate
Sample
  • Complex: Protein structure bound with substrates and lipids
    • Protein or peptide: Prestin
  • Ligand: 2-HYDROXYBENZOIC ACID
  • Ligand: CHOLESTEROL
Keywordstransporter family / membrane protein / lipid interaction / high resolution
Function / homology
Function and homology information


lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / response to thyroid hormone / negative regulation of monoatomic ion transmembrane transport / response to potassium ion ...lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / response to thyroid hormone / negative regulation of monoatomic ion transmembrane transport / response to potassium ion / response to auditory stimulus / chloride:bicarbonate antiporter activity / response to salt / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transport / Sensory processing of sound by outer hair cells of the cochlea / chloride transmembrane transporter activity / positive regulation of cell motility / spectrin binding / cochlea development / lateral plasma membrane / positive regulation of cell size / chloride transmembrane transport / response to ischemia / regulation of membrane potential / sensory perception of sound / regulation of cell shape / basolateral plasma membrane / response to xenobiotic stimulus / protein homodimerization activity / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsGe J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2021
Title: Molecular mechanism of prestin electromotive signal amplification.
Authors: Jingpeng Ge / Johannes Elferich / Sepehr Dehghani-Ghahnaviyeh / Zhiyu Zhao / Marc Meadows / Henrique von Gersdorff / Emad Tajkhorshid / Eric Gouaux /
Abstract: Hearing involves two fundamental processes: mechano-electrical transduction and signal amplification. Despite decades of studies, the molecular bases for both remain elusive. Here, we show how ...Hearing involves two fundamental processes: mechano-electrical transduction and signal amplification. Despite decades of studies, the molecular bases for both remain elusive. Here, we show how prestin, the electromotive molecule of outer hair cells (OHCs) that senses both voltage and membrane tension, mediates signal amplification by coupling conformational changes to alterations in membrane surface area. Cryoelectron microscopy (cryo-EM) structures of human prestin bound with chloride or salicylate at a common "anion site" adopt contracted or expanded states, respectively. Prestin is ensconced within a perimeter of well-ordered lipids, through which it induces dramatic deformation in the membrane and couples protein conformational changes to the bulk membrane. Together with computational studies, we illustrate how the anion site is allosterically coupled to changes in the transmembrane domain cross-sectional area and the surrounding membrane. These studies provide insight into OHC electromotility by providing a structure-based mechanism of the membrane motor prestin.
History
DepositionJan 21, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lh2
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23334.png

Downloads & links

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Map

FileDownload / File: emd_23334.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrestin in the presence of sodium salicylate and sodium sulfate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 256 pix.
= 166.579 Å		0.65 Å/pix.
x 256 pix.
= 166.579 Å		0.65 Å/pix.
x 256 pix.
= 166.579 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6507 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.07
Minimum - Maximum-0.23561147 - 0.43267477
Average (Standard dev.)0.005335016 (±0.025089333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 166.5792 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650699218750.650699218750.65069921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z166.579166.579166.579
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2360.4330.005

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Supplemental data

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Sample components

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Entire : Protein structure bound with substrates and lipids

EntireName: Protein structure bound with substrates and lipids
Components
  • Complex: Protein structure bound with substrates and lipids
    • Protein or peptide: Prestin
  • Ligand: 2-HYDROXYBENZOIC ACID
  • Ligand: CHOLESTEROL

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Supramolecule #1: Protein structure bound with substrates and lipids

SupramoleculeName: Protein structure bound with substrates and lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prestin

MacromoleculeName: Prestin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.064211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDHAEENEIL AATQRYYVER PIFSHPVLQE RLHTKDKVPD SIADKLKQAF TCTPKKIRNI IYMFLPITKW LPAYKFKEYV LGDLVSGIS TGVLQLPQGL AFAMLAAVPP IFGLYSSFYP VIMYCFLGTS RHISIGPFAV ISLMIGGVAV RLVPDDIVIP G GVNATNGT ...String:
MDHAEENEIL AATQRYYVER PIFSHPVLQE RLHTKDKVPD SIADKLKQAF TCTPKKIRNI IYMFLPITKW LPAYKFKEYV LGDLVSGIS TGVLQLPQGL AFAMLAAVPP IFGLYSSFYP VIMYCFLGTS RHISIGPFAV ISLMIGGVAV RLVPDDIVIP G GVNATNGT EARDALRVKV AMSVTLLSGI IQFCLGVCRF GFVAIYLTEP LVRGFTTAAA VHVFTSMLKY LFGVKTKRYS GI FSVVYST VAVLQNVKNL NVCSLGVGLM VFGLLLGGKE FNERFKEKLP APIPLEFFAV VMGTGISAGF NLKESYNVDV VGT LPLGLL PPANPDTSLF HLVYVDAIAI AIVGFSVTIS MAKTLANKHG YQVDGNQELI ALGLCNSIGS LFQTFSISCS LSRS LVQEG TGGKTQLAGC LASLMILLVI LATGFLFESL PQAVLSAIVI VNLKGMFMQF SDLPFFWRTS KIELTIWLTT FVSSL FLGL DYGLITAVII ALLTVIYRTQ SPSYKVLGKL PETDVYIDID AYEEVKEIPG IKIFQINAPI YYANSDLYSN ALKRKT GVN PAVIMGARRK AMRKYAKEVG NANMANATVV KADAEVDGED ATKPEEEDGE VKYPPIVIKS TFPEEMQRFM PPGDNVH TV ILDFTQVNFI DSVGVKTLAG IVKEYGDVGI YVYLAGCSAQ VVNDLTRNRF FENPALWELL FHSIHDAVLG SQLREALA E QEASAPPSQE DLEPNATPAT PEALEVLFQ

UniProtKB: Prestin

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Macromolecule #2: 2-HYDROXYBENZOIC ACID

MacromoleculeName: 2-HYDROXYBENZOIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: SAL
Molecular weightTheoretical: 138.121 Da
Chemical component information

ChemComp-SAL:
2-HYDROXYBENZOIC ACID

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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