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- EMDB-23331: Structure of human Prestin in nanodisc in the presence of NaCl -

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Basic information

Entry
Database: EMDB / ID: EMD-23331
TitleStructure of human Prestin in nanodisc in the presence of NaCl
Map dataPrestin in nanodisc in the presence of NaCl
Sample
  • Complex: Protein structure bound with substrates and lipids
    • Protein or peptide: Prestin
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: HEXANE
  • Ligand: HEPTANE
  • Ligand: TETRADECANE
  • Ligand: water
Keywordstransporter family / membrane protein / lipid interaction
Function / homology
Function and homology information


lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / response to potassium ion / response to auditory stimulus / chloride:bicarbonate antiporter activity ...lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / response to potassium ion / response to auditory stimulus / chloride:bicarbonate antiporter activity / response to thyroid hormone / response to salt / bicarbonate transport / bicarbonate transmembrane transporter activity / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of cell motility / chloride transport / chloride transmembrane transporter activity / spectrin binding / cochlea development / positive regulation of cell size / lateral plasma membrane / 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
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: 2.7 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 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lgw
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23331.png

Downloads & links

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Map

FileDownload / File: emd_23331.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrestin in nanodisc in the presence of NaCl
Voxel sizeX=Y=Z: 0.6507 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.44281775 - 0.8597254
Average (Standard dev.)0.004223485 (±0.0373308)
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-0.4430.8600.004

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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: CHLORIDE ION
  • Ligand: CHOLESTEROL
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: HEXANE
  • Ligand: HEPTANE
  • Ligand: TETRADECANE
  • Ligand: water

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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: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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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Macromolecule #4: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 4 / Number of copies: 38 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #5: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 5 / Number of copies: 33 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #6: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 6 / Number of copies: 10 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #7: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 7 / Number of copies: 2 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #8: HEPTANE

MacromoleculeName: HEPTANE / type: ligand / ID: 8 / Number of copies: 4 / Formula: HP6
Molecular weightTheoretical: 100.202 Da
Chemical component information

ChemComp-HP6:
HEPTANE

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Macromolecule #9: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 9 / Number of copies: 4 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 30 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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