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- EMDB-39563: The Cyro-EM Structure of human SLC26A3 with non-specific inhibito... -

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Basic information

Entry
Database: EMDB / ID: EMD-39563
TitleThe Cyro-EM Structure of human SLC26A3 with non-specific inhibitor Tenidap
Map data
Sample
  • Complex: The Cyo-EM structure of human SLC26A3 transporter with inhibitor Tenidap
    • Protein or peptide: Chloride anion exchanger
  • Ligand: 5-chloranyl-2-oxidanyl-3-thiophen-2-ylcarbonyl-indole-1-carboxamide
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsChloride anion exchanger / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity ...Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / monoatomic anion transport / membrane hyperpolarization / chloride transmembrane transporter activity / sperm capacitation / monoatomic ion transport / sperm midpiece / chloride transmembrane transport / cellular response to cAMP / brush border membrane / apical plasma membrane / 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
Chloride anion exchanger
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsFeng JR / Dang S
Funding support Hong Kong, 5 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)GRF16103321 Hong Kong
The University Grants Committee, Research Grants Council (RGC)GRF16102822 Hong Kong
The University Grants Committee, Research Grants Council (RGC)GRF16100223 Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6001-21EF Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6012-22GF Hong Kong
CitationJournal: To Be Published
Title: Structural Insights into the Inhibition Mechanism of Human DRA
Authors: Feng JR / Dang S
History
DepositionMar 22, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39563.png

Downloads & links

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Map

FileDownload / File: emd_39563.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.0091903 - 3.4133391
Average (Standard dev.)0.018249126 (±0.098596305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39563_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_39563_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_39563_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The Cyo-EM structure of human SLC26A3 transporter with inhibitor ...

EntireName: The Cyo-EM structure of human SLC26A3 transporter with inhibitor Tenidap
Components
  • Complex: The Cyo-EM structure of human SLC26A3 transporter with inhibitor Tenidap
    • Protein or peptide: Chloride anion exchanger
  • Ligand: 5-chloranyl-2-oxidanyl-3-thiophen-2-ylcarbonyl-indole-1-carboxamide
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: The Cyo-EM structure of human SLC26A3 transporter with inhibitor ...

SupramoleculeName: The Cyo-EM structure of human SLC26A3 transporter with inhibitor Tenidap
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.5 KDa

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Macromolecule #1: Chloride anion exchanger

MacromoleculeName: Chloride anion exchanger / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.591523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIEPFGNQYI VARPVYSTNA FEENHKKTGR HHKTFLDHLK VCCSCSPQKA KRIVLSLFPI ASWLPAYRLK EWLLSDIVSG ISTGIVAVL QGLAFALLVD IPPVYGLYAS FFPAIIYLFF GTSRHISVGP FPILSMMVGL AVSGAVSKAV PDRNATTLGL P NNSNNSSL ...String:
MIEPFGNQYI VARPVYSTNA FEENHKKTGR HHKTFLDHLK VCCSCSPQKA KRIVLSLFPI ASWLPAYRLK EWLLSDIVSG ISTGIVAVL QGLAFALLVD IPPVYGLYAS FFPAIIYLFF GTSRHISVGP FPILSMMVGL AVSGAVSKAV PDRNATTLGL P NNSNNSSL LDDERVRVAA AASVTVLSGI IQLAFGILRI GFVVIYLSES LISGFTTAAA VHVLVSQLKF IFQLTVPSHT DP VSIFKVL YSVFSQIEKT NIADLVTALI VLLVVSIVKE INQRFKDKLP VPIPIEFIMT VIAAGVSYGC DFKNRFKVAV VGD MNPGFQ PPITPDVETF QNTVGDCFGI AMVAFAVAFS VASVYSLKYD YPLDGNQELI ALGLGNIVCG VFRGFAGSTA LSRS AVQES TGGKTQIAGL IGAIIVLIVV LAIGFLLAPL QKSVLAALAL GNLKGMLMQF AEIGRLWRKD KYDCLIWIMT FIFTI VLGL GLGLAASVAF QLLTIVFRTQ FPKCSTLANI GRTNIYKNKK DYYDMYEPEG VKIFRCPSPI YFANIGFFRR KLIDAV GFS PLRILRKRNK ALRKIRKLQK QGLLQVTPKG FICTVDTIKD SDEELDNNQI EVLDQPINTT DLPFHIDWND DLPLNIE VP KISLHSLILD FSAVSFLDVS SVRGLKSILQ EFIRIKVDVY IVGTDDDFIE KLNRYEFFDG EVKSSIFFLT IHDAVLHI L MKKDYSTSKF NPSQEKDGKI DFTINTNGGL RNRVYEVPVE TKF

UniProtKB: Chloride anion exchanger

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Macromolecule #2: 5-chloranyl-2-oxidanyl-3-thiophen-2-ylcarbonyl-indole-1-carboxamide

MacromoleculeName: 5-chloranyl-2-oxidanyl-3-thiophen-2-ylcarbonyl-indole-1-carboxamide
type: ligand / ID: 2 / Number of copies: 2 / Formula: I2U
Molecular weightTheoretical: 320.751 Da
Chemical component information

ChemComp-I2U:
5-chloranyl-2-oxidanyl-3-thiophen-2-ylcarbonyl-indole-1-carboxamide

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTris-HClTris(hydroxymethyl)aminomethane
0.005 %GDNglyco-diosgenin
50.0 uMTenidaptenidap

Details: 25 mM Tris-HCl,150 mM NaCl,0.005% GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 45
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: blot with filter paper for 3-4 seconds before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3684 / Average exposure time: 4.5 sec. / Average electron dose: 51.2 e/Å2
Details: Images were collected in movie-mode containing 40 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. v1.18) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0))
Number images used: 550549
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0))
Final angle assignmentType: MAXIMUM LIKELIHOOD
Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0))

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Atomic model buiding 1

Initial modelPDB ID:

0879


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8ys8:
The Cyro-EM Structure of human SLC26A3 with non-specific inhibitor Tenidap

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