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- PDB-7xlm: Human diastrophic dysplasia sulfate transporter SLC26A2 -

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Basic information

Entry
Database: PDB / ID: 7xlm
TitleHuman diastrophic dysplasia sulfate transporter SLC26A2
ComponentsSulfate transporter
KeywordsTRANSPORT PROTEIN / Transporter / sulfate
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsChi, X.M. / Zhou, Q.
Funding support China, 1items
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, X.M. / Li, X.R. / Huang, B.D. / Zhou, Q.
History
DepositionApr 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jul 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin
Item: _citation.country / _citation.journal_id_ISSN / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfate transporter
B: Sulfate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,7404
Polymers176,5482
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sulfate transporter / Diastrophic dysplasia protein / Solute carrier family 26 member 2


Mass: 88273.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A2, DTD, DTDST / Production host: Homo sapiens (human) / References: UniProt: P50443
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human diastrophic dysplasia sulfate transporter SLC26A2
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395589 / Symmetry type: POINT

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