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- PDB-7wl9: Mouse Pendrin in chloride and bicarbonate in asymmetric state -

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Basic information

Entry
Database: PDB / ID: 7wl9
TitleMouse Pendrin in chloride and bicarbonate in asymmetric state
ComponentsPendrin
KeywordsTRANSPORT PROTEIN / exchange / transport / slc
Function / homology
Function and homology information


Multifunctional anion exchangers / inorganic anion transport / iodide transmembrane transporter activity / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / regulation of pH / chloride:bicarbonate antiporter activity / bicarbonate transmembrane transporter activity ...Multifunctional anion exchangers / inorganic anion transport / iodide transmembrane transporter activity / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / 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 / animal organ morphogenesis / brush border membrane / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsLiu, Q.Y. / Zhang, X. / Sun, L. / Chen, Z.G.
Funding support1items
OrganizationGrant numberCountry
Not funded81900729
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pendrin
B: Pendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5753
Polymers171,5392
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Pendrin / Sodium-independent chloride/iodide transporter / Solute carrier family 26 member 4


Mass: 85769.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc26a4, Pds / Production host: Homo sapiens (human) / References: UniProt: Q9R155
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
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: mouse Pendrin in chloride and bicarbonate in asymmetric state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353288 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210395
ELECTRON MICROSCOPYf_angle_d0.40314128
ELECTRON MICROSCOPYf_dihedral_angle_d13.1723714
ELECTRON MICROSCOPYf_chiral_restr0.0371716
ELECTRON MICROSCOPYf_plane_restr0.0031757

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