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- EMDB-38002: Cryo-EM structure of human DRA (SLC26A3) bound with oxalate -

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Basic information

Entry
Database: EMDB / ID: EMD-38002
TitleCryo-EM structure of human DRA (SLC26A3) bound with oxalate
Map datafull map
Sample
  • Complex: DRA
    • Protein or peptide: Chloride anion exchanger
  • Ligand: OXALATE ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: TETRADECANE
  • Ligand: DODECANE
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DECANE
  • Ligand: CHOLESTEROL
  • Ligand: water
KeywordsDRA / SLC26A3 / oxalate / TRANSPORT 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: 2.21 Å
AuthorsYang X / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human DRA (SLC26A3) bound with oxalate
Authors: Yang X / Zhang Y
History
DepositionNov 8, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38002.png

Downloads & links

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Map

FileDownload / File: emd_38002.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.5467224 - 5.1776357
Average (Standard dev.)0.0047795856 (±0.11864011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38002_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_38002_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half b

Fileemd_38002_half_map_2.map
Annotationhalf b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DRA

EntireName: DRA
Components
  • Complex: DRA
    • Protein or peptide: Chloride anion exchanger
  • Ligand: OXALATE ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: TETRADECANE
  • Ligand: DODECANE
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DECANE
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: DRA

SupramoleculeName: DRA / type: complex / 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 / Details: oxalate,lipids / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.877844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG TMIEPFGNQY IVARPVYSTN AFEENHKKTG RHHKTFLDHL KVCCSCSPQK AKRIVLSLFP IASWLPAYRL KEWLLSDIV SGISTGIVAV LQGLAFALLV DIPPVYGLYA SFFPAIIYLF FGTSRHISVG PFPILSMMVG LAVSGAVSKA V PDRNATTL ...String:
MDYKDDDDKG TMIEPFGNQY IVARPVYSTN AFEENHKKTG RHHKTFLDHL KVCCSCSPQK AKRIVLSLFP IASWLPAYRL KEWLLSDIV SGISTGIVAV LQGLAFALLV DIPPVYGLYA SFFPAIIYLF FGTSRHISVG PFPILSMMVG LAVSGAVSKA V PDRNATTL GLPNNSNNSS LLDDERVRVA AAASVTVLSG IIQLAFGILR IGFVVIYLSE SLISGFTTAA AVHVLVSQLK FI FQLTVPS HTDPVSIFKV LYSVFSQIEK TNIADLVTAL IVLLVVSIVK EINQRFKDKL PVPIPIEFIM TVIAAGVSYG CDF KNRFKV AVVGDMNPGF QPPITPDVET FQNTVGDCFG IAMVAFAVAF SVASVYSLKY DYPLDGNQEL IALGLGNIVC GVFR GFAGS TALSRSAVQE STGGKTQIAG LIGAIIVLIV VLAIGFLLAP LQKSVLAALA LGNLKGMLMQ FAEIGRLWRK DKYDC LIWI MTFIFTIVLG LGLGLAASVA FQLLTIVFRT QFPKCSTLAN IGRTNIYKNK KDYYDMYEPE GVKIFRCPSP IYFANI GFF RRKLIDAVGF SPLRILRKRN KALRKIRKLQ KQGLLQVTPK GFICTVDTIK DSDEELDNNQ IEVLDQPINT TDLPFHI DW NDDLPLNIEV PKISLHSLIL DFSAVSFLDV SSVRGLKSIL QEFIRIKVDV YIVGTDDDFI EKLNRYEFFD GEVKSSIF F LTIHDAVLHI LMKKDYSTSK FNPSQEKDGK IDFTINTNGG LRNRVYEVPV ETKF

UniProtKB: Chloride anion exchanger

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Macromolecule #2: OXALATE ION

MacromoleculeName: OXALATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: OXL
Molecular weightTheoretical: 88.019 Da
Chemical component information

ChemComp-OXL:
OXALATE ION

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 8 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #5: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 5 / Number of copies: 16 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #6: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 14 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

ChemComp-LPE:
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Macromolecule #7: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 7 / Number of copies: 38 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #8: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 18 / 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

Concentration12 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 4193 / Average exposure time: 3.51 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
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 correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 498096
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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