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- EMDB-74142: Structure of an Engineered Sodium/Iodide Symporter (PF-NIS) -

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Basic information

Entry
Database: EMDB / ID: EMD-74142
TitleStructure of an Engineered Sodium/Iodide Symporter (PF-NIS)
Map dataPF-NIS at 2.58A in presence of ReO4- and Na
Sample
  • Complex: Transporter
    • Protein or peptide: Sodium/iodide cotransporter
  • Ligand: PERRHENATE
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsNIS iodide SLC5A5 perrhenate / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium:iodide symporter activity / iodide transmembrane transport / Thyroxine biosynthesis / cellular response to Thyroid stimulating hormone / Organic anion transport by SLC5/17/25 transporters / monoatomic anion:sodium symporter activity / iodide transmembrane transporter activity / iodide transport / cellular response to gonadotropin stimulus / thyroid hormone generation ...sodium:iodide symporter activity / iodide transmembrane transport / Thyroxine biosynthesis / cellular response to Thyroid stimulating hormone / Organic anion transport by SLC5/17/25 transporters / monoatomic anion:sodium symporter activity / iodide transmembrane transporter activity / iodide transport / cellular response to gonadotropin stimulus / thyroid hormone generation / symporter activity / sodium ion transport / cellular response to forskolin / cellular response to cAMP / protein homodimerization activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Sodium/iodide cotransporter / : / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
Sodium/iodide cotransporter
Similarity search - Component
Biological speciesRattus (rats) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLlorente-Esteban A / Sabbineni H / Hoffsmith K / Manville RW / Lopez-Gonzalez D / Reyna-Neyra A / Leyva JA / Abbott GW / Bianchet MA / Carrasco N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114250 United States
CitationJournal: To Be Published
Title: Engineering substrate selectivity in the human sodium/iodide symporter (NIS)
Authors: Llorente-Esteban A / Sabbineni H / Hoffsmith K / Manville RW / Lopez-Gonzalez D / Reyna-Neyra A / Leyva JA / Abbott GW / Bianchet MA / Carrasco N
History
DepositionDec 1, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74142.png

Downloads & links

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Map

FileDownload / File: emd_74142.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPF-NIS at 2.58A in presence of ReO4- and Na
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 232.92 Å		0.65 Å/pix.
x 360 pix.
= 232.92 Å		0.65 Å/pix.
x 360 pix.
= 232.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.54932183 - 0.64514637
Average (Standard dev.)0.000013668469 (±0.014590917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 232.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74142_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74142_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_74142_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 : Transporter

EntireName: Transporter
Components
  • Complex: Transporter
    • Protein or peptide: Sodium/iodide cotransporter
  • Ligand: PERRHENATE
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Transporter

SupramoleculeName: Transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus (rats)

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Macromolecule #1: Sodium/iodide cotransporter

MacromoleculeName: Sodium/iodide cotransporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 65.308949 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGAEAGARA TFGAWDYGVF ATMLLVSTGI GLWVGLARGG QRSADDFFTG GRQLAAVPVG LSLAASFMSA VQVLGVPAEA ARYGLKFLW MCAGQLLNSL LTAFLFLPIF YRLGLTSTYQ YLELRFSRAV RLCGTLQYLV ATMLYTGIVI YAPALILNQV T GLDIWASL ...String:
MEGAEAGARA TFGAWDYGVF ATMLLVSTGI GLWVGLARGG QRSADDFFTG GRQLAAVPVG LSLAASFMSA VQVLGVPAEA ARYGLKFLW MCAGQLLNSL LTAFLFLPIF YRLGLTSTYQ YLELRFSRAV RLCGTLQYLV ATMLYTGIVI YAPALILNQV T GLDIWASL LSTGIICTLY TTVGGMKAVV WTDVFQVVVM LVGFWVILAR GVILLGGPRN VLSLAQQHSR INLMDFDPDP RS RYTFWTF IVGGTPFWLS MYGVNQAQVQ RYVACHTEGK AKLALLVNQL GLFLIVASAA CCGIVMFVYY KDCDPLLTGR ISA PDQYMP LLVLDIFEDL PGVPGLFLAC AYSGTLSTAS TSINAMAAVT VEDLIKPRMP GLAPRKLVFI SKGLSFIYGS ACLT VAALS SLLGGGVLQG SFTVMGVISG PLLGAFTLGM LLPACNTPGV LSGLAAGLAV SLWVAVGATL YPPGEQTMGV LPTSA AGCT QDSVLLGPPG ATQASNGIPS SGMDTGRPAL ADTFYAISYL YYGALGTLTT MLCGALISYL TGPTKRSSLG PGLLWW DLA RQTASVAPKE DTATLEESLV KGPEDIPAVT KKPPGLKPGA ETHPLYLGHD VETNL

UniProtKB: Sodium/iodide cotransporter

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Macromolecule #2: PERRHENATE

MacromoleculeName: PERRHENATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: REO
Molecular weightTheoretical: 250.205 Da
Chemical component information

ChemComp-REO:
PERRHENATE

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 21 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: We used the Ab-inito job of CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 461777
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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