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- EMDB-33469: Down-regulated in adenoma in complex with TQR1122 -

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Basic information

Entry
Database: EMDB / ID: EMD-33469
TitleDown-regulated in adenoma in complex with TQR1122
Map data
Sample
  • Cell: Down-regulated in adenoma
    • Protein or peptide: Chloride anion exchanger
  • Ligand: 2-[4,8-dimethyl-2-oxidanylidene-7-[[3-(trifluoromethyl)phenyl]methoxy]chromen-3-yl]ethanoic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water
KeywordsInhibitor / Transporter / TRANSPORT PROTEIN
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: 2.76 Å
AuthorsLi XR / Chi XM / Zhang YY / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100975 China
CitationJournal: To Be Published
Title: structure of human SLC26A3 in complex with TQR1122
Authors: Li XR / Chi XM / Zhang YY / Zhou Q
History
DepositionMay 18, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33469.png

Downloads & links

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Map

FileDownload / File: emd_33469.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 216 pix.
= 234.792 Å		1.09 Å/pix.
x 216 pix.
= 234.792 Å		1.09 Å/pix.
x 216 pix.
= 234.792 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.07297581 - 0.1392817
Average (Standard dev.)0.00059551623 (±0.0048359865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 234.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33469_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_33469_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Down-regulated in adenoma

EntireName: Down-regulated in adenoma
Components
  • Cell: Down-regulated in adenoma
    • Protein or peptide: Chloride anion exchanger
  • Ligand: 2-[4,8-dimethyl-2-oxidanylidene-7-[[3-(trifluoromethyl)phenyl]methoxy]chromen-3-yl]ethanoic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water

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Supramolecule #1: Down-regulated in adenoma

SupramoleculeName: Down-regulated in adenoma / 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: 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: 2-[4,8-dimethyl-2-oxidanylidene-7-[[3-(trifluoromethyl)phenyl]met...

MacromoleculeName: 2-[4,8-dimethyl-2-oxidanylidene-7-[[3-(trifluoromethyl)phenyl]methoxy]chromen-3-yl]ethanoic acid
type: ligand / ID: 2 / Number of copies: 2 / Formula: I2L
Molecular weightTheoretical: 406.352 Da
Chemical component information

ChemComp-I2L:
2-[4,8-dimethyl-2-oxidanylidene-7-[[3-(trifluoromethyl)phenyl]methoxy]chromen-3-yl]ethanoic acid

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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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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ch1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 960010
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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