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- EMDB-44896: Human SCNN1B-SCNN1G ENaC dimers -

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Basic information

Entry
Database: EMDB / ID: EMD-44896
TitleHuman SCNN1B-SCNN1G ENaC dimers
Map dataMap of beta gamma ENaC dimers with Fabs and one of the two dimers masked.
Sample
  • Complex: Amiloride-sensitive sodium channel subunits BETA, and GAMMA in complex with 10D4 Fab
    • Complex: Human beta subunit isoform 1
      • Protein or peptide: Amiloride-sensitive sodium channel subunit beta
    • Complex: Human gamma subunit isoform 1
      • Protein or peptide: Amiloride-sensitive sodium channel subunit gamma
    • Complex: Fab fragment from 10D4 IgG
      • Protein or peptide: 10D4 Fab
      • Protein or peptide: 10D4 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIon channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory perception of salty taste / Sensory perception of salty taste / sensory perception of sour taste / neutrophil-mediated killing of bacterium / aldosterone metabolic process / leukocyte activation involved in inflammatory response / cellular response to vasopressin / cellular response to aldosterone / sodium channel complex / epithelial fluid transport ...sensory perception of salty taste / Sensory perception of salty taste / sensory perception of sour taste / neutrophil-mediated killing of bacterium / aldosterone metabolic process / leukocyte activation involved in inflammatory response / cellular response to vasopressin / cellular response to aldosterone / sodium channel complex / epithelial fluid transport / mucus secretion / sodium ion homeostasis / renal system process / artery smooth muscle contraction / neutrophil activation involved in immune response / multicellular organismal-level water homeostasis / potassium ion homeostasis / intracellular sodium ion homeostasis / cellular response to acidic pH / sodium ion import across plasma membrane / ligand-gated sodium channel activity / erythrocyte homeostasis / response to food / WW domain binding / monoatomic ion channel activity / sodium ion transmembrane transport / cytoplasmic vesicle membrane / Stimuli-sensing channels / regulation of blood pressure / multicellular organism growth / gene expression / apical plasma membrane / response to xenobiotic stimulus / external side of plasma membrane / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Epithelial sodium channel subunit beta / Epithelial sodium channel subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsHouser A / Baconguis I
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138862 United States
Cystic Fibrosis FoundationBACONG22G0 United States
National Science Foundation (NSF, United States)GVPRS0015B4 United States
CitationJournal: Structure / Year: 2025
Title: Structural insights into subunit-dependent functional regulation in epithelial sodium channels.
Authors: Alexandra Houser / Isabelle Baconguis /
Abstract: Epithelial sodium channels (ENaCs) play a crucial role in Na reabsorption in mammals. To date, four subunits have been identified-α, β, γ, and δ-believed to form different heteromeric complexes. ...Epithelial sodium channels (ENaCs) play a crucial role in Na reabsorption in mammals. To date, four subunits have been identified-α, β, γ, and δ-believed to form different heteromeric complexes. Currently, only the structure of the αβγ complex is known. To investigate the formation of channels with different subunit compositions and to determine how each subunit contributes to distinct channel properties, we co-expressed human δ, β, and γ. Using single-particle cryoelectron microscopy, we observed three distinct ENaC complexes. The structures unveil a pattern in which β and γ positions are conserved among the different complexes while the α position in αβγ trimer is occupied by either δ or another β. The δ subunit induces structural rearrangements in the γ subunit, which may contribute to the differences in channel activity between αβγ and δβγ channels. These structural changes provide molecular insights into how ENaC subunit composition modulates channel function.
History
DepositionMay 15, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44896.png

Downloads & links

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Map

FileDownload / File: emd_44896.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of beta gamma ENaC dimers with Fabs and one of the two dimers masked.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.18390238 - 0.45775765
Average (Standard dev.)0.0008643797 (±0.009604285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44896_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw map of beta gamma ENaC dimers. Collected...

Fileemd_44896_additional_1.map
AnnotationRaw map of beta gamma ENaC dimers. Collected with a raw pixel size of 0.413. Micrographs were F-cropped by 0.5, box size for particles is 440.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of masked single beta gamma dimer...

Fileemd_44896_additional_2.map
AnnotationSharpened map of masked single beta gamma dimer used for model building.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the raw unmasked map

Fileemd_44896_half_map_1.map
AnnotationHalf map A of the raw unmasked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the raw unmasked map

Fileemd_44896_half_map_2.map
AnnotationHalf map B of the raw unmasked 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 : Amiloride-sensitive sodium channel subunits BETA, and GAMMA in co...

EntireName: Amiloride-sensitive sodium channel subunits BETA, and GAMMA in complex with 10D4 Fab
Components
  • Complex: Amiloride-sensitive sodium channel subunits BETA, and GAMMA in complex with 10D4 Fab
    • Complex: Human beta subunit isoform 1
      • Protein or peptide: Amiloride-sensitive sodium channel subunit beta
    • Complex: Human gamma subunit isoform 1
      • Protein or peptide: Amiloride-sensitive sodium channel subunit gamma
    • Complex: Fab fragment from 10D4 IgG
      • Protein or peptide: 10D4 Fab
      • Protein or peptide: 10D4 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Amiloride-sensitive sodium channel subunits BETA, and GAMMA in co...

SupramoleculeName: Amiloride-sensitive sodium channel subunits BETA, and GAMMA in complex with 10D4 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: Fab fragment from 10D4 IgG

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Supramolecule #2: Human beta subunit isoform 1

SupramoleculeName: Human beta subunit isoform 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human gamma subunit isoform 1

SupramoleculeName: Human gamma subunit isoform 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Fab fragment from 10D4 IgG

SupramoleculeName: Fab fragment from 10D4 IgG / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2, #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amiloride-sensitive sodium channel subunit beta

MacromoleculeName: Amiloride-sensitive sodium channel subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.728891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHVKKYLLKG LHRLQKGPGY TYKELLVWYC DNTNTHGPKR IICEGPKKKA MWFLLTLLFA ALVCWQWGIF IRTYLSWEVS VSLSVGFKT MDFPAVTICN ASPFKYSKIK HLLKDLDELM EAVLERILAP ELSHANATRN LNFSIWNHTP LVLIDERNPH H PMVLDLFG ...String:
MHVKKYLLKG LHRLQKGPGY TYKELLVWYC DNTNTHGPKR IICEGPKKKA MWFLLTLLFA ALVCWQWGIF IRTYLSWEVS VSLSVGFKT MDFPAVTICN ASPFKYSKIK HLLKDLDELM EAVLERILAP ELSHANATRN LNFSIWNHTP LVLIDERNPH H PMVLDLFG DNHNGLTSSS ASEKICNAHG CKMAMRLCSL NRTQCTFRNF TSATQALTEW YILQATNIFA QVPQQELVEM SY PGEQMIL ACLFGAEPCN YRNFTSIFYP HYGNCYIFNW GMTEKALPSA NPGTEFGLKL ILDIGQEDYV PFLASTAGVR LML HEQRSY PFIRDEGIYA MSGTETSIGV LVDKLQRMGE PYSPCTVNGS EVPVQNFYSD YNTTYSIQAC LRSCFQDHMI RNCN CGHYL YPLPRGEKYC NNRDFPDWAH CYSDLQMSVA QRETCIGMCK ESCNDTQYKM TISMADWPSE ASEDWIFHVL SQERD QSTN ITLSRKGIVK LNIYFQEFNY RTIEESAANN IVWLLSNLGG QFGFWMGGSV LCLIEFGEII IDFVWITIIK LVALAK SLR QRRAQASYAG PPPTVAELVE AHTNFGFQPD TAPRSPNTGP YPSEQALPIP GTPPPNYDSL RLQPLDVIES DSEGDAI

UniProtKB: Epithelial sodium channel subunit beta

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Macromolecule #2: 10D4 Fab

MacromoleculeName: 10D4 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.890183 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)

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Macromolecule #3: Amiloride-sensitive sodium channel subunit gamma

MacromoleculeName: Amiloride-sensitive sodium channel subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.352984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPGEKIKAK IKKNLPVTGP QAPTIKELMR WYCLNTNTHG CRRIVVSRGR LRRLLWIGFT LTAVALILWQ CALLVFSFYT VSVSIKVHF RKLDFPAVTI CNINPYKYST VRHLLADLEQ ETREALKSLY GFPESRKRRE AESWNSVSEG KQPRFSHRIP L LIFDQDEK ...String:
MAPGEKIKAK IKKNLPVTGP QAPTIKELMR WYCLNTNTHG CRRIVVSRGR LRRLLWIGFT LTAVALILWQ CALLVFSFYT VSVSIKVHF RKLDFPAVTI CNINPYKYST VRHLLADLEQ ETREALKSLY GFPESRKRRE AESWNSVSEG KQPRFSHRIP L LIFDQDEK GKARDFFTGR KRKVGGSIIH KASNVMHIES KQVVGFQLCS NDTSDCATYT FSSGINAIQE WYKLHYMNIM AQ VPLEKKI NMSYSAEELL VTCFFDGVSC DARNFTLFHH PMHGNCYTFN NRENETILST SMGGSEYGLQ VILYINEEEY NPF LVSSTG AKVIIHRQDE YPFVEDVGTE IETAMVTSIG MHLTESFKLS EPYSQCTEDG SDVPIRNIYN AAYSLQICLH SCFQ TKMVE KCGCAQYSQP LPPAANYCNY QQHPNWMYCY YQLHRAFVQE ELGCQSVCKE ACSFKEWTLT TSLAQWPSVV SEKWL LPVL TWDQGRQVNK KLNKTDLAKL LIFYKDLNQR SIMESPANSI EMLLSNFGGQ LGLWMSCSVV CVIEIIEVFF IDFFSI IAR RQWQKAKEWW AWKQAPPCPE APRSPQGQDN PALDIDDDLP TFNSALHLPP ALGTQVPGTP PPKYNTLRLE RAFSNQL TD TQMLDEL

UniProtKB: Epithelial sodium channel subunit gamma

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Macromolecule #4: 10D4 Fab

MacromoleculeName: 10D4 Fab / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 6.230672 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration2.275 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMKClpotassium chloride
20.0 mMC8H18N2O4SHEPES
5.0 mMCaCl2calcium chloride

Details: Vitrobot blot parameters were set to a wait time of 0s, blot time of 2s, and a blot force of 1
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse sample of beta and gamma ENaC with 10D4 Fab for the beta subunit

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 6021 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1121564
Details: From blob picking in cryoSPARC with a box size of 440 with a maximum particle diameter of 250 and a minimum of 150. Minimum separation distance was 0.6 diameters
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wth

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1)
Details: Local Resolution with one of the dimers and the Fabs masked out
Number images used: 248323
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 150000 / Software - Name: cryoSPARC (ver. 4.3.1)
Details: 248,325 in the class used for final reconstruction and 58,610 particles in the other class
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6wth


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: OTHER
Output model

PDB-9btu:
Human SCNN1B-SCNN1G ENaC dimers

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