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- EMDB-33284: Human diastrophic dysplasia sulfate transporter SLC26A2 -

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Basic information

Entry
Database: EMDB / ID: EMD-33284
TitleHuman diastrophic dysplasia sulfate transporter SLC26A2
Map data
Sample
  • Complex: human diastrophic dysplasia sulfate transporter SLC26A2
    • Protein or peptide: Sulfate transporter
  • Ligand: SULFATE ION
KeywordsTransporter / sulfate / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective SLC26A2 causes chondrodysplasias / Transport and metabolism of PAPS / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / chondrocyte proliferation / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity ...Defective SLC26A2 causes chondrodysplasias / Transport and metabolism of PAPS / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / chondrocyte proliferation / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / microvillus membrane / chondrocyte differentiation / chloride transmembrane transport / apical plasma membrane / extracellular exosome / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsChi XM / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: Dian Zi Xian Wei Xue Bao / Year: 2023
Title: Structure of human diastrophic dysplasia sulfate transporter SLC26A2
Authors: Chi XM / Li XR / Huang BD / Zhou Q
History
DepositionApr 22, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33284.png

Downloads & links

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Map

FileDownload / File: emd_33284.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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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09834704 - 0.15094128
Average (Standard dev.)0.00064191944 (±0.0045500416)
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_33284_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_33284_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human diastrophic dysplasia sulfate transporter SLC26A2

EntireName: human diastrophic dysplasia sulfate transporter SLC26A2
Components
  • Complex: human diastrophic dysplasia sulfate transporter SLC26A2
    • Protein or peptide: Sulfate transporter
  • Ligand: SULFATE ION

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Supramolecule #1: human diastrophic dysplasia sulfate transporter SLC26A2

SupramoleculeName: human diastrophic dysplasia sulfate transporter SLC26A2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Sulfate transporter

MacromoleculeName: Sulfate transporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.273945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDHDGD YKDHDIDYKD DDDKGASSAW SHPQFEKGGG SGGGSGGSAW SHPQFEKGSA AAMSSESKEQ HNVSPRDSAE GNDSYPSGI HLELQRESST DFKQFETNDQ CRPYHRILIE RQEKSDTNFK EFVIKKLQKN CQCSPAKAKN MILGFLPVLQ W LPKYDLKK ...String:
MADYKDHDGD YKDHDIDYKD DDDKGASSAW SHPQFEKGGG SGGGSGGSAW SHPQFEKGSA AAMSSESKEQ HNVSPRDSAE GNDSYPSGI HLELQRESST DFKQFETNDQ CRPYHRILIE RQEKSDTNFK EFVIKKLQKN CQCSPAKAKN MILGFLPVLQ W LPKYDLKK NILGDVMSGL IVGILLVPQS IAYSLLAGQE PVYGLYTSFF ASIIYFLLGT SRHISVGIFG VLCLMIGETV DR ELQKAGY DNAHSAPSLG MVSNGSTLLN HTSDRICDKS CYAIMVGSTV TFIAGVYQVA MGFFQVGFVS VYLSDALLSG FVT GASFTI LTSQAKYLLG LNLPRTNGVG SLITTWIHVF RNIHKTNLCD LITSLLCLLV LLPTKELNEH FKSKLKAPIP IELV VVVAA TLASHFGKLH ENYNSSIAGH IPTGFMPPKV PEWNLIPSVA VDAIAISIIG FAITVSLSEM FAKKHGYTVK ANQEM YAIG FCNIIPSFFH CFTTSAALAK TLVKESTGCH TQLSGVVTAL VLLLVLLVIA PLFYSLQKSV LGVITIVNLR GALRKF RDL PKMWSISRMD TVIWFVTMLS SALLSTEIGL LVGVCFSIFC VILRTQKPKS SLLGLVEESE VFESVSAYKN LQIKPGI KI FRFVAPLYYI NKECFKSALY KQTVNPILIK VAWKKAAKRK IKEKVVTLGG IQDEMSVQLS HDPLELHTIV IDCSAIQF L DTAGIHTLKE VRRDYEAIGI QVLLAQCNPT VRDSLTNGEY CKKEEENLLF YSVYEAMAFA EVSKNQKGVC VPNGLSLSS D

UniProtKB: Sulfate transporter

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Macromolecule #2: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm
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: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 395589
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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