[English] 日本語
Yorodumi
- PDB-6wth: Full-length human ENaC ECD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wth
TitleFull-length human ENaC ECD
Components
  • (Amiloride-sensitive sodium channel subunit ...) x 3
  • 10D4 Fab
  • 7B1 Fab
KeywordsMEMBRANE PROTEIN / sodium channel / blood pressure / epithelial / salt transport
Function / homology
Function and homology information


: / : / sensory perception of salty taste / Sensory perception of salty taste / aldosterone metabolic process / neutrophil-mediated killing of bacterium / sensory perception of sour taste / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sperm principal piece ...: / : / sensory perception of salty taste / Sensory perception of salty taste / aldosterone metabolic process / neutrophil-mediated killing of bacterium / sensory perception of sour taste / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sperm principal piece / sodium channel complex / ligand-gated sodium channel activity / epithelial fluid transport / sodium ion homeostasis / artery smooth muscle contraction / mucus secretion / neutrophil activation involved in immune response / WW domain binding / cellular response to aldosterone / multicellular organismal-level water homeostasis / cellular response to acidic pH / potassium ion homeostasis / sodium ion import across plasma membrane / sodium channel activity / intracellular sodium ion homeostasis / motile cilium / erythrocyte homeostasis / ciliary membrane / response to food / sodium ion transport / sodium ion transmembrane transport / acrosomal vesicle / cytoplasmic vesicle membrane / multicellular organism growth / Stimuli-sensing channels / regulation of blood pressure / monoatomic ion channel activity / gene expression / response to xenobiotic stimulus / apical plasma membrane / external side of plasma membrane / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
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
Amiloride-sensitive sodium channel subunit alpha / Amiloride-sensitive sodium channel subunit beta / Amiloride-sensitive sodium channel subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsPosert, R. / Baconguis, I. / Noreng, S. / Bharadwaj, A. / Houser, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD017871 United States
American Heart Association19TPA34760754 United States
American Heart Association18PRE33990205 United States
National Science Foundation (NSF, United States)DGE-1937961 United States
CitationJournal: Elife / Year: 2020
Title: Molecular principles of assembly, activation, and inhibition in epithelial sodium channel.
Authors: Sigrid Noreng / Richard Posert / Arpita Bharadwaj / Alexandra Houser / Isabelle Baconguis /
Abstract: The molecular bases of heteromeric assembly and link between Na self-inhibition and protease-sensitivity in epithelial sodium channels (ENaCs) are not fully understood. Previously, we demonstrated ...The molecular bases of heteromeric assembly and link between Na self-inhibition and protease-sensitivity in epithelial sodium channels (ENaCs) are not fully understood. Previously, we demonstrated that ENaC subunits - α, β, and γ - assemble in a counterclockwise configuration when viewed from outside the cell with the protease-sensitive GRIP domains in the periphery (Noreng et al., 2018). Here we describe the structure of ENaC resolved by cryo-electron microscopy at 3 Å. We find that a combination of precise domain arrangement and complementary hydrogen bonding network defines the subunit arrangement. Furthermore, we determined that the α subunit has a primary functional module consisting of the finger and GRIP domains. The module is bifurcated by the α2 helix dividing two distinct regulatory sites: Na and the inhibitory peptide. Removal of the inhibitory peptide perturbs the Na site via the α2 helix highlighting the critical role of the α2 helix in regulating ENaC function.
History
DepositionMay 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21896
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amiloride-sensitive sodium channel subunit alpha
B: Amiloride-sensitive sodium channel subunit beta
C: Amiloride-sensitive sodium channel subunit gamma
D: 7B1 Fab
E: 7B1 Fab
F: 10D4 Fab
G: 10D4 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,77415
Polymers262,5937
Non-polymers2,1818
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Amiloride-sensitive sodium channel subunit ... , 3 types, 3 molecules ABC

#1: Protein Amiloride-sensitive sodium channel subunit alpha / Alpha-NaCH / Epithelial Na(+) channel subunit alpha / ENaCA / Nonvoltage-gated sodium channel 1 ...Alpha-NaCH / Epithelial Na(+) channel subunit alpha / ENaCA / Nonvoltage-gated sodium channel 1 subunit alpha / SCNEA


Mass: 75780.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCNN1A, SCNN1 / Production host: Homo sapiens (human) / References: UniProt: P37088
#2: Protein Amiloride-sensitive sodium channel subunit beta / Beta-NaCH / Epithelial Na(+) channel subunit beta / ENaCB / Nonvoltage-gated sodium channel 1 ...Beta-NaCH / Epithelial Na(+) channel subunit beta / ENaCB / Nonvoltage-gated sodium channel 1 subunit beta / SCNEB


Mass: 72728.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCNN1B / Production host: Homo sapiens (human) / References: UniProt: P51168
#3: Protein Amiloride-sensitive sodium channel subunit gamma / Epithelial Na(+) channel subunit gamma / Gamma-ENaC / Gamma-NaCH / Nonvoltage-gated sodium channel ...Epithelial Na(+) channel subunit gamma / Gamma-ENaC / Gamma-NaCH / Nonvoltage-gated sodium channel 1 subunit gamma / SCNEG


Mass: 74352.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCNN1G / Production host: Homo sapiens (human) / References: UniProt: P51170

-
Antibody , 2 types, 4 molecules DEFG

#4: Antibody 7B1 Fab


Mass: 10060.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#5: Antibody 10D4 Fab


Mass: 9805.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

-
Sugars , 2 types, 7 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Full-length human ENaC heterotrimer bound with two high-affinity Fabs
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.32 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T/17 / Plasmid: pBacMam
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K
Details: 3.5 uL applied, manual blot, fresh 3.5 uL applied, vitrobot blot and freeze

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252071 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211972
ELECTRON MICROSCOPYf_angle_d0.3916309
ELECTRON MICROSCOPYf_dihedral_angle_d12.2744046
ELECTRON MICROSCOPYf_chiral_restr0.0461884
ELECTRON MICROSCOPYf_plane_restr0.0022128

+
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://pdbjlvh1.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