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- EMDB-44674: Human SCNN1D-SCNN1B-SCNN1G ENaC trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-44674
TitleHuman SCNN1D-SCNN1B-SCNN1G ENaC trimer
Map data
Sample
  • Cell: Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA
    • Complex: Human delta subunit isoform 1
      • Protein or peptide: Isoform 1 of Amiloride-sensitive sodium channel subunit delta
    • Complex: Human beta subunit isoform 1
    • Complex: Human gamma subunit isoform 1
      • Protein or peptide: Amiloride-sensitive sodium channel subunit beta
  • Protein or peptide: Amiloride-sensitive sodium channel subunit gamma
  • 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 / sodium channel complex / epithelial fluid transport / mucus secretion ...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 / sodium channel complex / epithelial fluid transport / mucus secretion / sodium ion homeostasis / renal system process / artery smooth muscle contraction / neutrophil activation involved in immune response / cellular response to aldosterone / multicellular organismal-level water homeostasis / potassium ion homeostasis / cellular response to acidic pH / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / ligand-gated sodium channel activity / response to food / erythrocyte homeostasis / WW domain binding / sodium channel activity / monoatomic ion channel activity / sodium ion transmembrane transport / cytoplasmic vesicle membrane / multicellular organism growth / regulation of blood pressure / Stimuli-sensing channels / actin cytoskeleton / gene expression / apical plasma membrane / response to xenobiotic stimulus / external side of plasma membrane / extracellular exosome / nucleoplasm / membrane / 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 / Epithelial sodium channel subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 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 1, 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_44674.png

Downloads & links

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Map

FileDownload / File: emd_44674.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 440 pix.
= 352.66 Å		0.8 Å/pix.
x 440 pix.
= 352.66 Å		0.8 Å/pix.
x 440 pix.
= 352.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8015 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.17199042 - 0.3627018
Average (Standard dev.)0.00006429535 (±0.007881532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 352.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44674_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_44674_additional_1.map
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Half map: #1

Fileemd_44674_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_44674_half_map_2.map
Projections & Slices
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Sample components

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Entire : Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA

EntireName: Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA
Components
  • Cell: Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA
    • Complex: Human delta subunit isoform 1
      • Protein or peptide: Isoform 1 of Amiloride-sensitive sodium channel subunit delta
    • Complex: Human beta subunit isoform 1
    • Complex: Human gamma subunit isoform 1
      • Protein or peptide: Amiloride-sensitive sodium channel subunit beta
  • Protein or peptide: Amiloride-sensitive sodium channel subunit gamma
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA

SupramoleculeName: Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1

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Supramolecule #2: Human delta subunit isoform 1

SupramoleculeName: Human delta subunit isoform 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Contains mutation C64A in the predicted transmembrane domain. C64 is thought to be palmitoylated and effect gating.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.2 kDa/nm

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Supramolecule #3: Human beta subunit isoform 1

SupramoleculeName: Human beta subunit isoform 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Details: Contains mutation C30A in the predicted transmembrane domain. C30 is thought to be palmitoylated and effect gating.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.6 kDa/nm

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Supramolecule #4: Human gamma subunit isoform 1

SupramoleculeName: Human gamma subunit isoform 1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Details: Contains mutations C33A and C41A in the predicted transmembrane domain. C333 and C41 are thought to be palmitoylated and effect gating. Additionally R138 is mutated to alanine. This residue ...Details: Contains mutations C33A and C41A in the predicted transmembrane domain. C333 and C41 are thought to be palmitoylated and effect gating. Additionally R138 is mutated to alanine. This residue is hypothesized to be key in gating by proteolysis.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.1 kDa/nm

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Macromolecule #1: Isoform 1 of Amiloride-sensitive sodium channel subunit delta

MacromoleculeName: Isoform 1 of Amiloride-sensitive sodium channel subunit delta
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.273773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEHRSMDGR MEAATRGGSH LQAAAQTPPR PGPPSAPPPP PKEGHQEGLV ELPASFRELL TFFATNATIH GAIRLVCSRG NRLKTTSWG LLSLGALVAL CWQLGLLFER HWHRPVLMAV SVHSERKLLP LVTLCDGNPR RPSPVLRHLE LLDEFARENI D SLYNVNLS ...String:
MAEHRSMDGR MEAATRGGSH LQAAAQTPPR PGPPSAPPPP PKEGHQEGLV ELPASFRELL TFFATNATIH GAIRLVCSRG NRLKTTSWG LLSLGALVAL CWQLGLLFER HWHRPVLMAV SVHSERKLLP LVTLCDGNPR RPSPVLRHLE LLDEFARENI D SLYNVNLS KGRAALSATV PRHEPPFHLD REIRLQRLSH SGSRVRVGFR LCNSTGGDCF YRGYTSGVAA VQDWYHFHYV DI LALLPAA WEDSHGSQDG HFVLSCSYDG LDCQARQFRT FHHPTYGSCY TVDGVWTAQR PGITHGVGLV LRVEQQPHLP LLS TLAGIR VMVHGRNHTP FLGHHSFSVR PGTEATISIR EDEVHRLGSP YGHCTAGGEG VEVELLHNTS YTRQACLVSC FQQL MVETC SCGYYLHPLP AGAEYCSSAR HPAWGHCFYR LYQDLETHRL PCTSRCPRPC RESAFKLSTG TSRWPSAKSA GWTLA TLGE QGLPHQSHRQ RSSLAKINIV YQELNYRSVE EAPVYSVPQL LSAMGSLCSL WFGASVLSLL ELLELLLDAS ALTLVL GGR RLRRAWFSWP RASPASGASS IKPEASQMPP PAGGTSDDPE PSGPHLPRVM LPGVLAGVSA EESWAGPQPL ETLDT

UniProtKB: Epithelial sodium channel subunit delta

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Macromolecule #2: Amiloride-sensitive sodium channel subunit beta

MacromoleculeName: Amiloride-sensitive sodium channel subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.696828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHVKKYLLKG LHRLQKGPGY TYKELLVWYA DNTNTHGPKR IICEGPKKKA MWFLLTLLFA ALVCWQWGIF IRTYLSWEVS VSLSVGFKT MDFPAVTICN ASPFKYSKIK HLLKDLDELM EAVLERILAP ELSHANATRN LNFSIWNHTP LVLIDERNPH H PMVLDLFG ...String:
MHVKKYLLKG LHRLQKGPGY TYKELLVWYA 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 #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: 74.202742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPGEKIKAK IKKNLPVTGP QAPTIKELMR WYALNTNTHG ARRIVVSRGR LRRLLWIGFT LTAVALILWQ CALLVFSFYT VSVSIKVHF RKLDFPAVTI CNINPYKYST VRHLLADLEQ ETREALKSLY GFPESRKRAE AESWNSVSEG KQPRFSHRIP L LIFDQDEK ...String:
MAPGEKIKAK IKKNLPVTGP QAPTIKELMR WYALNTNTHG ARRIVVSRGR LRRLLWIGFT LTAVALILWQ CALLVFSFYT VSVSIKVHF RKLDFPAVTI CNINPYKYST VRHLLADLEQ ETREALKSLY GFPESRKRAE 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 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / 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

Concentration3.44 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 delta, 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: 18108 / 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 165 and a minimum of 140. Minimum separation distance was 0.6 diameters
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wth

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 193373
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: 100000 / Software - Name: cryoSPARC (ver. 4.3.1)
Details: 193,373 in the class used for final reconstruction and 21,574 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-9blr:
Human SCNN1D-SCNN1B-SCNN1G ENaC trimer

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