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- PDB-6bqn: Cryo-EM structure of ENaC -

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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 / sensory perception of sour taste / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / aldosterone metabolic process / cellular response to vasopressin / sperm principal piece / sodium channel complex / ligand-gated sodium channel activity ...sensory perception of salty taste / Sensory perception of salty taste / sensory perception of sour taste / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / aldosterone metabolic process / cellular response to vasopressin / sperm principal piece / sodium channel complex / ligand-gated sodium channel activity / epithelial fluid transport / sodium ion homeostasis / mucus secretion / artery smooth muscle contraction / renal system process / neutrophil activation involved in immune response / cellular response to aldosterone / multicellular organismal-level water homeostasis / cellular response to acidic pH / sodium ion import across plasma membrane / potassium ion homeostasis / intracellular sodium ion homeostasis / motile cilium / sodium channel activity / erythrocyte homeostasis / response to food / ciliary membrane / WW domain binding / sodium ion transport / monoatomic ion channel activity / sodium ion transmembrane transport / acrosomal vesicle / cytoplasmic vesicle membrane / multicellular organism growth / Stimuli-sensing channels / regulation of blood pressure / 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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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
Water00
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

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Components

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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)

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Details

Has protein modificationY
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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Membrane protein complex / 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

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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)

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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

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