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- PDB-7lgu: Structure of human prestin in the presence of NaCl -

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Basic information

Entry
Database: PDB / ID: 7lgu
TitleStructure of human prestin in the presence of NaCl
ComponentsPrestin
KeywordsMEMBRANE PROTEIN / transporter family / 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 salt / response to thyroid hormone / bicarbonate transport / bicarbonate transmembrane transporter activity / positive regulation of cell motility / Sensory processing of sound by outer hair cells of the cochlea / 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
TETRADECANE / CHOLESTEROL / DECANE / DODECANE / HEXANE / HEPTANE / N-OCTANE / Prestin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsGe, J. / Gouaux, E.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2May 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,876112
Polymers164,1282
Non-polymers14,748110
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47550 Å2
ΔGint506 kcal/mol
Surface area59060 Å2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 82064.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A5, PRES / Production host: Homo sapiens (human) / References: UniProt: P58743

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Non-polymers , 9 types, 221 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical...
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical...
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical
ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H16
#9: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Protein structure bound with substrates and lipids / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K

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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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311620
ELECTRON MICROSCOPYf_angle_d0.53315392
ELECTRON MICROSCOPYf_dihedral_angle_d18.5182138
ELECTRON MICROSCOPYf_chiral_restr0.0861744
ELECTRON MICROSCOPYf_plane_restr0.0031808

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