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Yorodumi- EMDB-32580: Mouse Pendrin in chloride and iodide buffer in asymmetric state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32580 | |||||||||
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Title | Mouse Pendrin in chloride and iodide buffer in asymmetric state | |||||||||
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Sample |
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Keywords | exchange / transport / slc / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information Multifunctional anion exchangers / inorganic anion transport / iodide transmembrane transporter activity / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / iodide transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / regulation of pH / chloride:bicarbonate antiporter activity ...Multifunctional anion exchangers / inorganic anion transport / iodide transmembrane transporter activity / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / iodide transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / regulation of pH / chloride:bicarbonate antiporter activity / 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 | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Liu QY / Zhang X / Sun L / Chen ZG | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32580.map.gz | 104.3 MB | EMDB map data format | |
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Header (meta data) | emd-32580-v30.xml emd-32580.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_32580.png | 100.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32580 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32580 | HTTPS FTP |
-Related structure data
Related structure data | 7wlbMC 7wk1C 7wk7C 7wl2C 7wl7C 7wl8C 7wl9C 7wlaC 7wleC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32580.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : mouse Pendrin in chloride and bicarbonate in inward state
Entire | Name: mouse Pendrin in chloride and bicarbonate in inward state |
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Components |
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-Supramolecule #1: mouse Pendrin in chloride and bicarbonate in inward state
Supramolecule | Name: mouse Pendrin in chloride and bicarbonate in inward state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Pendrin
Macromolecule | Name: Pendrin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 85.769578 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45859 |