[English] 日本語
Yorodumi
- PDB-6bqn: Cryo-EM structure of ENaC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bqn
TitleCryo-EM structure of ENaC
Components
  • (10D4 fab) x 2
  • (7B1 fab) x 2
  • EGFP-SCNN1G chimera
  • SCNN1A
  • SCNN1B
KeywordsMEMBRANE PROTEIN / sodium channel
Function / homology
Function and homology information


: / : / sensory perception of salty taste / Sensory perception of salty taste / aldosterone metabolic process / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sensory perception of sour taste / sodium channel complex ...: / : / sensory perception of salty taste / Sensory perception of salty taste / aldosterone metabolic process / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sensory perception of sour taste / sodium channel complex / sperm principal piece / 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 / cellular response to acidic pH / multicellular organismal-level water homeostasis / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / sodium channel activity / potassium ion homeostasis / motile cilium / erythrocyte homeostasis / response to food / ciliary membrane / sodium ion transport / sodium ion transmembrane transport / acrosomal vesicle / multicellular organism growth / cytoplasmic vesicle membrane / 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 / cytosol / cytoplasm
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: 3.9 Å
AuthorsNoreng, S. / Bharadwaj, A. / Posert, R. / Yoshioka, C. / Baconguis, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director United States
CitationJournal: Elife / Year: 2018
Title: Structure of the human epithelial sodium channel by cryo-electron microscopy.
Authors: Sigrid Noreng / Arpita Bharadwaj / Richard Posert / Craig Yoshioka / Isabelle Baconguis /
Abstract: The epithelial sodium channel (ENaC), a member of the ENaC/DEG superfamily, regulates Na and water homeostasis. ENaCs assemble as heterotrimeric channels that harbor protease-sensitive domains ...The epithelial sodium channel (ENaC), a member of the ENaC/DEG superfamily, regulates Na and water homeostasis. ENaCs assemble as heterotrimeric channels that harbor protease-sensitive domains critical for gating the channel. Here, we present the structure of human ENaC in the uncleaved state determined by single-particle cryo-electron microscopy. The ion channel is composed of a large extracellular domain and a narrow transmembrane domain. The structure reveals that ENaC assembles with a 1:1:1 stoichiometry of α:β:γ subunits arranged in a counter-clockwise manner. The shape of each subunit is reminiscent of a hand with key gating domains of a 'finger' and a 'thumb.' Wedged between these domains is the elusive protease-sensitive inhibitory domain poised to regulate conformational changes of the 'finger' and 'thumb'; thus, the structure provides the first view of the architecture of inhibition of ENaC.
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-7130
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7130
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SCNN1A
B: SCNN1B
C: EGFP-SCNN1G chimera
D: 7B1 fab
E: 7B1 fab
F: 10D4 fab
G: 10D4 fab


Theoretical massNumber of molelcules
Total (without water)203,6227
Polymers203,6227
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy, Fluorescence size-exclusion chromatography used to detect shift in addition to visually seeing the complex by single particle cryo-electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Antibody , 7 types, 7 molecules ABCDEFG

#1: Antibody SCNN1A


Mass: 54038.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Transmembrane helices have been built with poly UNK since the density for the transmembrane domain is not good enough to accurately build a model. Residues that have not been built is due to ...Details: Transmembrane helices have been built with poly UNK since the density for the transmembrane domain is not good enough to accurately build a model. Residues that have not been built is due to flexible areas of the protein where density is missing. The full sequence is described in sequence details.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P37088*PLUS
#2: Antibody SCNN1B


Mass: 55038.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Transmembrane helices have been built with poly UNK since the density for the transmembrane domain is not good enough to accurately build a model. Residues that have not been built is due to ...Details: Transmembrane helices have been built with poly UNK since the density for the transmembrane domain is not good enough to accurately build a model. Residues that have not been built is due to flexible areas of the protein where density is missing. The full sequence is described in sequence details.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P51168*PLUS
#3: Antibody EGFP-SCNN1G chimera


Mass: 55834.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is EGFP-SCNN1G chimera. Transmembrane helices have been built with poly UNK since the density for the transmembrane domain is not good enough to accurately build a model. ...Details: The protein is EGFP-SCNN1G chimera. Transmembrane helices have been built with poly UNK since the density for the transmembrane domain is not good enough to accurately build a model. Residues that have not been built is due to flexible areas of the protein where density is missing. The first 260 residues is a His8 tag and a strep-tag followed by EGFP (UniProt accession code: C5MKY7). The full sequence is described in sequence details.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P51170*PLUS
#4: Antibody 7B1 fab


Mass: 9039.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unknown, built with poly UNK. / Source: (natural) Mus musculus (house mouse)
#5: Antibody 7B1 fab


Mass: 10315.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unknown, built with poly UNK. / Source: (natural) Mus musculus (house mouse)
#6: Antibody 10D4 fab


Mass: 9805.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unknown, built with poly UNK. / Source: (natural) Mus musculus (house mouse)
#7: Antibody 10D4 fab


Mass: 9549.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unknown, built with poly UNK. / Source: (natural) Mus musculus (house mouse)

-
Details

Sequence detailsThe sequence of SCNNIA is MAEEEALIEFHRSYRELFEFFANNTTIHGAIRLVSSQHNRMKTAFWAVLWLATFGMMYWQFGLLFGEY ...The sequence of SCNNIA is MAEEEALIEFHRSYRELFEFFANNTTIHGAIRLVSSQHNRMKTAFWAVLWLATFGMMYWQFGLLFGEY FSYPVSLNINLNSDKLVFPAVTICTLNPYRYPEIKEELEELDRITEQTLFDLYKYSSFTTLVAGSRSR ADLRGTLPHPLQALAVPPPPHGAAAAASVASSLRDNNPQVDWKDWKIGFQLCNQNKSDCFYQTYSSGV DAVAEWYAFHYINILSRLPETLPSLEEDTLGNFIFACRFNQVSCNQANYSHFHHPMYGNCYTFNDKNN SNLWMSSMPGINNGLSLMLRAEQNDFIPLLSTVTGARVMVHGQDEPAFMDDGGFNLRPGVETSISMRK ETLDRLGGDYGDCTKNGSDVPVENLYPSKYTQQVCIHSCFQESMIKECGCAYIFYPRPQNVEYCDYRK HSSWGYCYYKLQVDFSSDHLGCFTKCRKPCSVTSYQLSAGYSRWPSVTSQEWVFQMLSRQNNYTVNNK RNGVAKVNIFFKELNYKTNSESPSVTMVTLLSNLGSQWSLWFGSSVLSVVEMAELVFDLLVIM The seuqnce of SCNN1B is MADNTNTHGPKRIIKEGPKKKAMWFLLTLLFAALVCWQWGIFIRTYLSWEVSVSLSVGFKTMDFPAVT ICNASPFKYSKIKHLLKDLDELMEAVLERILAPELSHANATRNLNFSIWNHTPLVLIDERNPHHPMVL DLFGDNHNGLTSSSASEKICNAHGCKMAMRLCSLNRTQCTFRNFTSATQALTEWYILQATNIFAQVPQ QELVEMSYPGEQMILACLFGAEPCNYRNFTSIFYPHYGNCYIFNWGMTEKALPSANPGTEFGLKLILD IGQEDYVPFLASTAGVRLMLHEQRSYPFIRDEGIYAMSGTETSIGVLVDKLQRMGEPYSPCTVNGSEV PVQNFYSDYNTTYSIQACLRSCFQDHMIRNCNCGHYLYPLPRGEKYCNNRDFPDWAHCYSDLQMSVAQ RETCIGMCKESCNDTQYKMTISMADWPSEASEDWIFHVLSQERDQSTNITLSRKGIVKLNIYFQEFNY RTIEESAANNIVWLLSNLGGQFGFWMGGSVLALIEFGEIIIDFVWITIIKLVALAKS The sequence of EGFP-SCNN1G chimera is MHHHHHHHHAAAWSHPQFEKGGSMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYTTRAEV KFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLAD HYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKSGLRSGLVPR GGRQAPTIKELMRWYALNTNTHGIRRIVVSRGRLRRLLWIGFTLTAVALILWQCALLVFSFYTVSVSI KVHFRKLDFPAVTICNINPYKYSTVRHLLADLEQETREALKSLYGFPESAAAAEAESWNSVSEGKQPR FSHRIPLLIFDQDEKGKARDFFTGQQQQVGGSIIHKASNVMHIESKQVVGFQLCSNDTSDCATYTFSS GINAIQEWYKLHYMNIMAQVPLEKKINMSYSAEELLVTCFFDGVSCDARNFTLFHHPMHGNCYTFNNR ENETILSTSMGGSEYGLQVILYINEEEYNPFLVSSTGAKVIIHRQDEYPFVEDVGTEIETAMVTSIGM HLTESFKLSEPYSQCTEDGSDVPIRNIYNAAYSLQICLHSCFQTKMVEKCGCAQYSQPLPPAANYCNY QQHPNWMYCYYQLHRAFVQEELGCQSVCKEACSFKEWTLTTSLAQWPSVVSEKWLLPVLTWDQGRQVN KKLNKTDLAKLLIFYKDLNQRSIMESPANSIEMLLSNFGGQLGLWMSCSVVAVIEIIEVFFIDFFSII ARRQWQKAK

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Membrane protein complexBiological membrane / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304615 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312984
ELECTRON MICROSCOPYf_angle_d0.65617781
ELECTRON MICROSCOPYf_dihedral_angle_d6.1167739
ELECTRON MICROSCOPYf_chiral_restr0.042062
ELECTRON MICROSCOPYf_plane_restr0.0052345

+
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