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- EMDB-33473: Human SLC26A3 in complex with Tenidap -

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Basic information

Entry
Database: EMDB / ID: EMD-33473
TitleHuman SLC26A3 in complex with Tenidap
Map data
Sample
  • Cell: human SLC26A3 in complex with Tenidap
    • Protein or peptide: Chloride anion exchanger
  • Ligand: 5-chloranyl-2-oxidanyl-3-thiophen-2-ylcarbonyl-indole-1-carboxamide
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsInhibitor / Transporter / PROTEIN TRANSPORT
Function / homology
Function and homology information


Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) / Multifunctional anion exchangers / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / membrane hyperpolarization / bicarbonate transmembrane transporter activity ...Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) / Multifunctional anion exchangers / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / membrane hyperpolarization / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transmembrane transporter activity / sperm capacitation / monoatomic ion transport / cellular response to cAMP / sperm midpiece / 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: 3.16 Å
AuthorsLi XR / Chi XM / Zhang YY / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: To Be Published
Title: Structure of human SLC26A3 in complex with Tenidap
Authors: Li XR / Chi XM / Zhang YY / Zhou Q
History
DepositionMay 18, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33473.png

Downloads & links

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Map

FileDownload / File: emd_33473.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 344.64 Å		1.08 Å/pix.
x 320 pix.
= 344.64 Å		1.08 Å/pix.
x 320 pix.
= 344.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.048397023 - 0.105054334
Average (Standard dev.)0.000097159325 (±0.0021701797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33473_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33473_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human SLC26A3 in complex with Tenidap

EntireName: human SLC26A3 in complex with Tenidap
Components
  • Cell: human SLC26A3 in complex with 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: human SLC26A3 in complex with Tenidap

SupramoleculeName: human SLC26A3 in complex with Tenidap / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 79.333672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QYIVARPVYS TNAFEENHKK TGRHHKTFLD HLKVCCSCSP QKAKRIVLSL FPIASWLPAY RLKEWLLSDI VSGISTGIVA VLQGLAFAL LVDIPPVYGL YASFFPAIIY LFFGTSRHIS VGPFPILSMM VGLAVSGAVS KAVPDRNATT LGLPNNSNNS S LLDDERVR ...String:
QYIVARPVYS TNAFEENHKK TGRHHKTFLD HLKVCCSCSP QKAKRIVLSL FPIASWLPAY RLKEWLLSDI VSGISTGIVA VLQGLAFAL LVDIPPVYGL YASFFPAIIY LFFGTSRHIS VGPFPILSMM VGLAVSGAVS KAVPDRNATT LGLPNNSNNS S LLDDERVR VAAAASVTVL SGIIQLAFGI LRIGFVVIYL SESLISGFTT AAAVHVLVSQ LKFIFQLTVP SHTDPVSIFK VL YSVFSQI EKTNIADLVT ALIVLLVVSI VKEINQRFKD KLPVPIPIEF IMTVIAAGVS YGCDFKNRFK VAVVGDMNPG FQP PITPDV ETFQNTVGDC FGIAMVAFAV AFSVASVYSL KYDYPLDGNQ ELIALGLGNI VCGVFRGFAG STALSRSAVQ ESTG GKTQI AGLIGAIIVL IVVLAIGFLL APLQKSVLAA LALGNLKGML MQFAEIGRLW RKDKYDCLIW IMTFIFTIVL GLGLG LAAS VAFQLLTIVF RTQFPKCSTL ANIGRTNIYK NKKDYYDMYE PEGVKIFRCP SPIYFANIGF FRRKLIDAVG FSPLRI LRK RNKALRKIRK LQKQGLLQVT PKGFICTVDT IKDSDEELDN NQIEVLDQPI NTTDLPFHID WNDDLPLNIE VPKISLH SL ILDFSAVSFL DVSSVRGLKS ILQEFIRIKV DVYIVGTDDD FIEKLNRYEF FDGEVKSSIF FLTIHDAVLH ILMKKD

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 783905
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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