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- PDB-9ikv: human SLC26A7 with iodide -

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Basic information

Entry
Database: PDB / ID: 9ikv
Titlehuman SLC26A7 with iodide
ComponentsAnion exchange transporter
KeywordsTRANSPORT PROTEIN / substrate / transporter
Function / homology
Function and homology information


gluconate transmembrane transport / oxalate transport / nitrate transmembrane transport / Multifunctional anion exchangers / gastric acid secretion / iodide transport / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / chloride:bicarbonate antiporter activity ...gluconate transmembrane transport / oxalate transport / nitrate transmembrane transport / Multifunctional anion exchangers / gastric acid secretion / iodide transport / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / chloride:bicarbonate antiporter activity / thyroid hormone generation / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / chloride transport / chloride channel activity / lateral plasma membrane / monoatomic ion transport / chloride transmembrane transport / recycling endosome membrane / basolateral plasma membrane / endosome / apical plasma membrane / plasma membrane / cytoplasm
Similarity search - Function
SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
IODIDE ION / Anion exchange transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi, X. / Yang, X. / Lu, X. / Lin, B. / Zhang, Y. / Huang, B. / Zhou, Y. / Huang, J. / Wu, K. / Zhou, Q. / Chi, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32100975 China
CitationJournal: To Be Published
Title: human SLC26A7 with iodide
Authors: Li, X. / Yang, X. / Lu, X. / Lin, B. / Zhang, Y. / Huang, B. / Zhou, Y. / Huang, J. / Wu, K. / Zhou, Q. / Chi, X.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anion exchange transporter
B: Anion exchange transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0596
Polymers144,5512
Non-polymers5084
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Anion exchange transporter / Solute carrier family 26 member 7


Mass: 72275.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A7, SUT2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8TE54
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: Complex of human SLC26A7 in complex with iodide / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 493875 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038840
ELECTRON MICROSCOPYf_angle_d0.54812028
ELECTRON MICROSCOPYf_dihedral_angle_d4.0871190
ELECTRON MICROSCOPYf_chiral_restr0.0411452
ELECTRON MICROSCOPYf_plane_restr0.0031472

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