7TJ8

Cryo-EM structure of the human Nax channel in complex with beta3 solved in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-guided unlocking of Na X reveals a non-selective tetrodotoxin-sensitive cation channel.

Noland, C.L.Chua, H.C.Kschonsak, M.Heusser, S.A.Braun, N.Chang, T.Tam, C.Tang, J.Arthur, C.P.Ciferri, C.Pless, S.A.Payandeh, J.

(2022) Nat Commun 13: 1416-1416

  • DOI: https://doi.org/10.1038/s41467-022-28984-4
  • Primary Citation of Related Structures:  
    7TJ8, 7TJ9

  • PubMed Abstract: 

    Unlike classical voltage-gated sodium (Na V ) channels, Na X has been characterized as a voltage-insensitive, tetrodotoxin-resistant, sodium (Na + )-activated channel involved in regulating Na + homeostasis. However, Na X remains refractory to functional characterization in traditional heterologous systems. Here, to gain insight into its atypical physiology, we determine structures of the human Na X channel in complex with the auxiliary β3-subunit. Na X reveals structural alterations within the selectivity filter, voltage sensor-like domains, and pore module. We do not identify an extracellular Na + -sensor or any evidence for a Na + -based activation mechanism in Na X . Instead, the S6-gate remains closed, membrane lipids fill the central cavity, and the domain III-IV linker restricts S6-dilation. We use protein engineering to identify three pore-wetting mutations targeting the hydrophobic S6-gate that unlock a robust voltage-insensitive leak conductance. This constitutively active Na X -QTT channel construct is non-selective among monovalent cations, inhibited by extracellular calcium, and sensitive to classical Na V channel blockers, including tetrodotoxin. Our findings highlight a functional diversity across the Na V channel scaffold, reshape our understanding of Na X physiology, and provide a template to demystify recalcitrant ion channels.


  • Organizational Affiliation

    Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 7 subunit alpha1,737Homo sapiensMutation(s): 0 
Gene Names: SCN7ASCN6A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01118 (Homo sapiens)
Explore Q01118 
Go to UniProtKB:  Q01118
PHAROS:  Q01118
GTEx:  ENSG00000136546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01118
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-3215Homo sapiensMutation(s): 0 
Gene Names: SCN3BKIAA1158
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY72 (Homo sapiens)
Explore Q9NY72 
Go to UniProtKB:  Q9NY72
PHAROS:  Q9NY72
GTEx:  ENSG00000166257 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NY72
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth A]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
PEV
Query on PEV

Download Ideal Coordinates CCD File 
C [auth A],
G [auth A],
O [auth A]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
Q [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
F [auth A]
H [auth A]
I [auth A]
K [auth A]
L [auth A]
F [auth A],
H [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
N [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release