6XIW

Cryo-EM structure of the sodium leak channel NALCN-FAM155A complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the human sodium leak channel NALCN.

Kschonsak, M.Chua, H.C.Noland, C.L.Weidling, C.Clairfeuille, T.Bahlke, O.O.Ameen, A.O.Li, Z.R.Arthur, C.P.Ciferri, C.Pless, S.A.Payandeh, J.

(2020) Nature 587: 313-318

  • DOI: https://doi.org/10.1038/s41586-020-2570-8
  • Primary Citation of Related Structures:  
    6XIW

  • PubMed Abstract: 

    Persistently depolarizing sodium (Na + ) leak currents enhance electrical excitability 1,2 . The ion channel responsible for the major background Na + conductance in neurons is the Na + leak channel, non-selective (NALCN) 3,4 . NALCN-mediated currents regulate neuronal excitability linked to respiration, locomotion and circadian rhythm 4-10 . NALCN activity is under tight regulation 11-14 and mutations in NALCN cause severe neurological disorders and early death 15,16 . NALCN is an orphan channel in humans, and fundamental aspects of channel assembly, gating, ion selectivity and pharmacology remain obscure. Here we investigate this essential leak channel and determined the structure of NALCN in complex with a distinct auxiliary subunit, family with sequence similarity 155 member A (FAM155A). FAM155A forms an extracellular dome that shields the ion-selectivity filter from neurotoxin attack. The pharmacology of NALCN is further delineated by a walled-off central cavity with occluded lateral pore fenestrations. Unusual voltage-sensor domains with asymmetric linkages to the pore suggest mechanisms by which NALCN activity is modulated. We found a tightly closed pore gate in NALCN where the majority of missense patient mutations cause gain-of-function phenotypes that cluster around the S6 gate and distinctive π-bulges. Our findings provide a framework to further study the physiology of NALCN and a foundation for discovery of treatments for NALCN channelopathies and other electrical disorders.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium leak channel non-selective protein1,794Homo sapiensMutation(s): 0 
Gene Names: NALCNVGCNL1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZF0 (Homo sapiens)
Explore Q8IZF0 
Go to UniProtKB:  Q8IZF0
PHAROS:  Q8IZF0
GTEx:  ENSG00000102452 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZF0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein FAM155A483Homo sapiensMutation(s): 0 
Gene Names: FAM155A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for B1AL88 (Homo sapiens)
Explore B1AL88 
Go to UniProtKB:  B1AL88
PHAROS:  B1AL88
GTEx:  ENSG00000204442 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1AL88
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGV
Query on PGV

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
PEV
Query on PEV

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
A
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM1.02
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-11-25
    Changes: Database references, Structure summary