[English] 日本語
Yorodumi
- EMDB-44889: Human SCNN1B-SCNN1B-SCNN1G ENaC trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44889
TitleHuman SCNN1B-SCNN1B-SCNN1G ENaC trimer
Map dataMap of beta, beta, gamma ENaC with Fab masked, collected with a raw pixel size of 0.40075. Micrographs were F-cropped by 0.5, box size for particles is 440.
Sample
  • Cell: Amiloride-sensitive sodium channel subunits DELTA, BETA, and GAMMA
    • 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
  • 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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

-
Structure visualization

Supplemental images

emd_44889.png

Downloads & links

-
Map

FileDownload / File: emd_44889.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of beta, beta, gamma ENaC with Fab masked, collected with a raw pixel size of 0.40075. Micrographs were F-cropped by 0.5, box size for particles is 440.
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: 0.0583
Minimum - Maximum-0.17730749 - 0.4307419
Average (Standard dev.)0.00010032387 (±0.008873978)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_44889_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened primary map used from CryoSPARC used for model building

Fileemd_44889_additional_1.map
AnnotationSharpened primary map used from CryoSPARC used for model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B of the raw unmasked map

Fileemd_44889_half_map_1.map
AnnotationHalf map B of the raw unmasked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A of the raw unmasked map

Fileemd_44889_half_map_2.map
AnnotationHalf map A of the raw unmasked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
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-#2

-
Supramolecule #2: Human beta subunit isoform 1

SupramoleculeName: Human beta subunit isoform 1 / type: complex / ID: 2 / 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)

-
Supramolecule #3: Human gamma subunit isoform 1

SupramoleculeName: Human gamma subunit isoform 1 / type: complex / ID: 3 / 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)

-
Macromolecule #1: Amiloride-sensitive sodium channel subunit beta

MacromoleculeName: Amiloride-sensitive sodium channel subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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

-
Macromolecule #2: Amiloride-sensitive sodium channel subunit gamma

MacromoleculeName: Amiloride-sensitive sodium channel subunit gamma / type: protein_or_peptide / ID: 2 / 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

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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: 3.12 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 342011
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: 3 / Avg.num./class: 200000 / Software - Name: cryoSPARC (ver. 4.3.1)
Details: 342,011 in the class used for final reconstruction and 166,617 particles in one class, 193,040 classes in the other that were not used.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6wth


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

PDB-9btg:
Human SCNN1B-SCNN1B-SCNN1G ENaC trimer

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more