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- EMDB-35393: Human SLC26A3 in the apo state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35393
TitleHuman SLC26A3 in the apo state
Map data
Sample
  • Cell: Human SLC26A3 in the apo state
    • Protein or peptide: Chloride anion exchanger
KeywordsTransporter / MEMBRANE 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: 3.5 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: Human SLC26A3 in the apo state
Authors: Li XR / Chi XM / Zhang YY / Zhou Q
History
DepositionFeb 15, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35393.png

Downloads & links

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Map

FileDownload / File: emd_35393.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 215.4 Å		1.08 Å/pix.
x 200 pix.
= 215.4 Å		1.08 Å/pix.
x 200 pix.
= 215.4 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: 0.04
Minimum - Maximum-0.19688904 - 0.30666178
Average (Standard dev.)0.0008054166 (±0.00997798)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 215.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35393_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35393_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 : Human SLC26A3 in the apo state

EntireName: Human SLC26A3 in the apo state
Components
  • Cell: Human SLC26A3 in the apo state
    • Protein or peptide: Chloride anion exchanger

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Supramolecule #1: Human SLC26A3 in the apo state

SupramoleculeName: Human SLC26A3 in the apo state / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
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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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 (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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 142727
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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