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- PDB-7x1g: Cryo-EM structure of human BTR1 in the inward-facing state at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 7x1g
TitleCryo-EM structure of human BTR1 in the inward-facing state at pH 5.5
ComponentsIsoform 1 of Solute carrier family 4 member 11
KeywordsMEMBRANE PROTEIN / SLC4A11 / BTR1 / SLC transporter
Function / homology
Function and homology information


borate transport / active borate transmembrane transporter activity / regulation of mesenchymal stem cell differentiation / fluid transport / water transmembrane transporter activity / monoatomic ion homeostasis / intracellular monoatomic cation homeostasis / cellular hypotonic response / proton channel activity / solute:inorganic anion antiporter activity ...borate transport / active borate transmembrane transporter activity / regulation of mesenchymal stem cell differentiation / fluid transport / water transmembrane transporter activity / monoatomic ion homeostasis / intracellular monoatomic cation homeostasis / cellular hypotonic response / proton channel activity / solute:inorganic anion antiporter activity / symporter activity / vesicle membrane / sodium channel activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / sodium ion transport / proton transmembrane transporter activity / transmembrane transporter activity / proton transmembrane transport / regulation of mitochondrial membrane potential / transmembrane transport / cellular response to oxidative stress / basolateral plasma membrane / protein dimerization activity / apical plasma membrane / plasma membrane
Similarity search - Function
Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter family / Phosphotransferase/anion transporter
Similarity search - Domain/homology
Solute carrier family 4 member 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYin, Y. / Lu, Y. / Zuo, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030081 China
National Natural Science Foundation of China (NSFC)81874235 China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the conformational changes of BTR1/SLC4A11 in complex with PIP.
Authors: Yishuo Lu / Peng Zuo / Hongyi Chen / Hui Shan / Weize Wang / Zonglin Dai / He Xu / Yayu Chen / Ling Liang / Dian Ding / Yan Jin / Yuxin Yin /
Abstract: BTR1 (SLC4A11) is a NH stimulated H (OH) transporter belonging to the SLC4 family. Dysfunction of BTR1 leads to diseases such as congenital hereditary endothelial dystrophy (CHED) and Fuchs ...BTR1 (SLC4A11) is a NH stimulated H (OH) transporter belonging to the SLC4 family. Dysfunction of BTR1 leads to diseases such as congenital hereditary endothelial dystrophy (CHED) and Fuchs endothelial corneal dystrophy (FECD). However, the mechanistic basis of BTR1 activation by alkaline pH, transport activity regulation and pathogenic mutations remains elusive. Here, we present cryo-EM structures of human BTR1 in the outward-facing state in complex with its activating ligands PIP and the inward-facing state with the pathogenic R125H mutation. We reveal that PIP binds at the interface between the transmembrane domain and the N-terminal cytosolic domain of BTR1. Disruption of either the PIP binding site or protonation of PIP phosphate groups by acidic pH can transform BTR1 into an inward-facing conformation. Our results provide insights into the mechanisms of how the transport activity and conformation changes of BTR1 are regulated by PIP binding and interaction of TMD and NTD.
History
DepositionFeb 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: 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

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Solute carrier family 4 member 11
B: Isoform 1 of Solute carrier family 4 member 11


Theoretical massNumber of molelcules
Total (without water)199,3692
Polymers199,3692
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform 1 of Solute carrier family 4 member 11 / Sodium borate cotransporter 1 / NaBC1 / Solute carrier family 4 member 11 / isoform B


Mass: 99684.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC4A11, BTR1 / Production host: Homo sapiens (human) / References: UniProt: Q8NBS3

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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: Solute carrier family 4 member 11, isoform B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.199 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 5.5
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 FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 3.1.0 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161085 / Symmetry type: POINT

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