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- EMDB-32577: Mouse Pendrin in chloride and iodide buffer in inward state -

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Basic information

Entry
Database: EMDB / ID: EMD-32577
TitleMouse Pendrin in chloride and iodide buffer in inward state
Map data
Sample
  • Complex: mouse Pendrin in chloride and iodide buffer in inward state
    • Protein or peptide: Pendrin
Keywordsexchange / transport / slc / TRANSPORT PROTEIN
Function / homology
Function and homology information


Multifunctional anion exchangers / inorganic anion transport / iodide transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transporter activity / iodide transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / regulation of pH ...Multifunctional anion exchangers / inorganic anion transport / iodide transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transporter activity / iodide transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / regulation of pH / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / brush border membrane / animal organ morphogenesis / regulation of protein localization / apical plasma membrane / extracellular exosome / membrane / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu QY / Zhang X / Sun L / Chen ZG
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970146 China
CitationJournal: Nat Commun / Year: 2023
Title: Asymmetric pendrin homodimer reveals its molecular mechanism as anion exchanger.
Authors: Qianying Liu / Xiang Zhang / Hui Huang / Yuxin Chen / Fang Wang / Aihua Hao / Wuqiang Zhan / Qiyu Mao / Yuxia Hu / Lin Han / Yifang Sun / Meng Zhang / Zhimin Liu / Geng-Lin Li / Weijia Zhang ...Authors: Qianying Liu / Xiang Zhang / Hui Huang / Yuxin Chen / Fang Wang / Aihua Hao / Wuqiang Zhan / Qiyu Mao / Yuxia Hu / Lin Han / Yifang Sun / Meng Zhang / Zhimin Liu / Geng-Lin Li / Weijia Zhang / Yilai Shu / Lei Sun / Zhenguo Chen /
Abstract: Pendrin (SLC26A4) is an anion exchanger expressed in the apical membranes of selected epithelia. Pendrin ablation causes Pendred syndrome, a genetic disorder associated with sensorineural hearing ...Pendrin (SLC26A4) is an anion exchanger expressed in the apical membranes of selected epithelia. Pendrin ablation causes Pendred syndrome, a genetic disorder associated with sensorineural hearing loss, hypothyroid goiter, and reduced blood pressure. However its molecular structure has remained unknown, limiting our understanding of the structural basis of transport. Here, we determine the cryo-electron microscopy structures of mouse pendrin with symmetric and asymmetric homodimer conformations. The asymmetric homodimer consists of one inward-facing protomer and the other outward-facing protomer, representing coincident uptake and secretion- a unique state of pendrin as an electroneutral exchanger. The multiple conformations presented here provide an inverted alternate-access mechanism for anion exchange. The structural and functional data presented here disclose the properties of an anion exchange cleft and help understand the importance of disease-associated variants, which will shed light on the pendrin exchange mechanism.
History
DepositionJan 12, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32577.png

Downloads & links

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Map

FileDownload / File: emd_32577.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.010436597 - 1.3362032
Average (Standard dev.)0.0006275111 (±0.015496748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : mouse Pendrin in chloride and iodide buffer in inward state

EntireName: mouse Pendrin in chloride and iodide buffer in inward state
Components
  • Complex: mouse Pendrin in chloride and iodide buffer in inward state
    • Protein or peptide: Pendrin

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Supramolecule #1: mouse Pendrin in chloride and iodide buffer in inward state

SupramoleculeName: mouse Pendrin in chloride and iodide buffer in inward state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Pendrin

MacromoleculeName: Pendrin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 85.769578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAARGGRSEP PQLAEYSCSY TVSRPVYSEL AFQQQRERRL PERRTLRDSL ARSCSCSRKR AFGVVKTLLP ILDWLPKYRV KEWLLSDII SGVSTGLVGT LQGMAYALLA AVPVQFGLYS AFFPILTYFV FGTSRHISVG PFPVVSLMVG SVVLSMAPDD H FLVPSGNG ...String:
MAARGGRSEP PQLAEYSCSY TVSRPVYSEL AFQQQRERRL PERRTLRDSL ARSCSCSRKR AFGVVKTLLP ILDWLPKYRV KEWLLSDII SGVSTGLVGT LQGMAYALLA AVPVQFGLYS AFFPILTYFV FGTSRHISVG PFPVVSLMVG SVVLSMAPDD H FLVPSGNG SALNSTTLDT GTRDAARVLL ASTLTLLVGI IQLVFGGLQI GFIVRYLADP LVGGFTTAAA FQVLVSQLKI VL NVSTKNY NGILSIIYTL IEIFQNIGDT NIADFIAGLL TIIVCMAVKE LNDRFKHRIP VPIPIEVIVT IIATAISYGA NLE KNYNAG IVKSIPSGFL PPVLPSVGLF SDMLAASFSI AVVAYAIAVS VGKVYATKHD YVIDGNQEFI AFGISNVFSG FFSC FVATT ALSRTAVQES TGGKTQVAGL ISAVIVMVAI VALGRLLEPL QKSVLAAVVI ANLKGMFMQV CDVPRLWKQN KTDAV IWVF TCIMSIILGL DLGLLAGLLF ALLTVVLRVQ FPSWNGLGSV PSTDIYKSIT HYKNLEEPEG VKILRFSSPI FYGNVD GFK KCINSTVGFD AIRVYNKRLK ALRRIQKLIK KGQLRATKNG IISDIGSSNN AFEPDEDVEE PEELNIPTKE IEIQVDW NS ELPVKVNVPK VPIHSLVLDC GAVSFLDVVG VRSLRMIVKE FQRIDVNVYF ALLQDDVLEK MEQCGFFDDN IRKDRFFL T VHDAILHLQN QVKSREGQDS LLETVARIRD CKDPLDLMEA EMNAEELDVQ DEAMRRLAS

UniProtKB: Pendrin

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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

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Electron microscopy

MicroscopeFEI TITAN 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: 2.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79043

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