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- EMDB-32942: Cryo-EM structure of human BTR1 in the outward-facing state. -

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Basic information

Entry
Database: EMDB / ID: EMD-32942
TitleCryo-EM structure of human BTR1 in the outward-facing state.
Map dataSharpened map of wild-type BTR1
Sample
  • Complex: Solute carrier family 4 member 11, isoform B
    • Protein or peptide: Isoform 1 of Solute carrier family 4 member 11
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
KeywordsSLC4A11 / BTR1 / SLC transporter / MEMBRANE PROTEIN
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 transmembrane transporter activity / bicarbonate transport / monoatomic anion transport / sodium ion transport / transmembrane transporter activity / proton 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYin Y / Lu Y / Zuo P
Funding support China, 2 items
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, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32942.png

Downloads & links

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Map

FileDownload / File: emd_32942.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of wild-type BTR1
Voxel sizeX=Y=Z: 0.821 Å
Density
Contour LevelBy AUTHOR: 0.256
Minimum - Maximum-0.75884765 - 1.2276847
Average (Standard dev.)0.00045954433 (±0.026111502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-A map of wild-type BTR1

Fileemd_32942_half_map_1.map
AnnotationHalf-A map of wild-type BTR1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B map of wild-type BTR1

Fileemd_32942_half_map_2.map
AnnotationHalf-B map of wild-type BTR1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Solute carrier family 4 member 11, isoform B

EntireName: Solute carrier family 4 member 11, isoform B
Components
  • Complex: Solute carrier family 4 member 11, isoform B
    • Protein or peptide: Isoform 1 of Solute carrier family 4 member 11
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate

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Supramolecule #1: Solute carrier family 4 member 11, isoform B

SupramoleculeName: Solute carrier family 4 member 11, isoform B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 199 KDa

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Macromolecule #1: Isoform 1 of Solute carrier family 4 member 11

MacromoleculeName: Isoform 1 of Solute carrier family 4 member 11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.684438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQVGGRGDR CTQEVQGLVH GAGDLSASLA ENSPTMSQNG YFEDSSYYKC DTDDTFEARE EILGDEAFDT ANSSIVSGES IRFFVNVNL EMQATNTENE ATSGGCVLLH TSRKYLKLKN FKEEIRAHRD LDGFLAQASI VLNETATSLD NVLRTMLRRF A RDPDNNEP ...String:
MSQVGGRGDR CTQEVQGLVH GAGDLSASLA ENSPTMSQNG YFEDSSYYKC DTDDTFEARE EILGDEAFDT ANSSIVSGES IRFFVNVNL EMQATNTENE ATSGGCVLLH TSRKYLKLKN FKEEIRAHRD LDGFLAQASI VLNETATSLD NVLRTMLRRF A RDPDNNEP NCNLDLLMAM LFTDAGAPMR GKVHLLSDTI QGVTATVTGV RYQQSWLCII CTMKALQKRH VCISRLVRPQ NW GENSCEV RFVILVLAPP KMKSTKTAME VARTFATMFS DIAFRQKLLE TRTEEEFKEA LVHQRQLLTM VSHGPVAPRT KER STVSLP AHRHPEPPKC KDFVPFGKGI REDIARRFPL YPLDFTDGII GKNKAVGKYI TTTLFLYFAC LLPTIAFGSL NDEN TDGAI DVQKTIAGQS IGGLLYALFS GQPLVILLTT APLALYIQVI RVICDDYDLD FNSFYAWTGL WNSFFLALYA FFNLS LVMS LFKRSTEEII ALFISITFVL DAVKGTVKIF WKYYYGHYLD DYHTKRTSSL VSLSGLGASL NASLHTALNA SFLASP TEL PSATHSGQAT AVLSLLIMLG TLWLGYTLYQ FKKSPYLHPC VREILSDCAL PIAVLAFSLI SSHGFREIEM SKFRYNP SE SPFAMAQIQS LSLRAVSGAM GLGFLLSMLF FIEQNLVAAL VNAPENRLVK GTAYHWDLLL LAIINTGLSL FGLPWIHA A YPHSPLHVRA LALVEERVEN GHIYDTIVNV KETRLTSLGA SVLVGLSLLL LPVPLQWIPK PVLYGLFLYI ALTSLDGNQ LVQRVALLLK EQTAYPPTHY IRRVPQRKIH YFTGLQVLQL LLLCAFGMSS LPYMKMIFPL IMIAMIPIRY ILLPRIIEAK YLDVMDAEH RP

UniProtKB: Solute carrier family 4 member 11

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Macromolecule #2: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

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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: 7.5
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: 1.8 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 92740

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