7CM3 | pdb_00007cm3

Cryo-EM structure of human NALCN in complex with FAM155A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7CM3

This is version 1.3 of the entry. See complete history

Literature

Structure of the human sodium leak channel NALCN in complex with FAM155A.

Xie, J.Ke, M.Xu, L.Lin, S.Huang, J.Zhang, J.Yang, F.Wu, J.Yan, Z.

(2020) Nat Commun 11: 5831-5831

  • DOI: https://doi.org/10.1038/s41467-020-19667-z
  • Primary Citation Related Structures: 
    7CM3

  • PubMed Abstract: 

    NALCN, a sodium leak channel expressed mainly in the central nervous system, is responsible for the resting Na + permeability that controls neuronal excitability. Dysfunctions of the NALCN channelosome, NALCN with several auxiliary subunits, are associated with a variety of human diseases. Here, we report the cryo-EM structure of human NALCN in complex with FAM155A at an overall resolution of 3.1 angstroms. FAM155A forms extensive interactions with the extracellular loops of NALCN that may help stabilize NALCN in the membrane. A Na + ion-binding site, reminiscent of a Ca 2+ binding site in Ca v channels, is identified in the unique EEKE selectivity filter. Despite its 'leaky' nature, the channel is closed and the intracellular gate is sealed by S6 I , II-III linker and III-IV linker. Our study establishes the molecular basis of Na + permeation and voltage sensitivity, and provides important clues to the mechanistic understanding of NALCN regulation and NALCN channelosome-related diseases.


  • Organizational Affiliation
    • Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China.

Macromolecule Content 

  • Total Structure Weight: 267.58 kDa 
  • Atom Count: 12,418 
  • Modeled Residue Count: 1,460 
  • Deposited Residue Count: 2,250 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium leak channel non-selective protein1,765Homo 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
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q8IZF0-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane protein FAM155A485Homo 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: B1AL88-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
(Subject of Investigation/LOI)

Query on PC1



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A],
P [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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection