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- PDB-7cm3: Cryo-EM structure of human NALCN in complex with FAM155A -

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Basic information

Entry
Database: PDB / ID: 7cm3
TitleCryo-EM structure of human NALCN in complex with FAM155A
Components
  • Sodium leak channel non-selective protein
  • Transmembrane protein FAM155ATransmembrane protein
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


stretch-activated, monoatomic cation-selective, calcium channel activity / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / sodium channel activity / voltage-gated sodium channel activity / monoatomic ion channel complex / calcium ion import across plasma membrane / sodium ion transmembrane transport / monoatomic cation channel activity ...stretch-activated, monoatomic cation-selective, calcium channel activity / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / sodium channel activity / voltage-gated sodium channel activity / monoatomic ion channel complex / calcium ion import across plasma membrane / sodium ion transmembrane transport / monoatomic cation channel activity / potassium ion transmembrane transport / monoatomic ion transmembrane transport / positive regulation of synaptic transmission, GABAergic / calcium ion transmembrane transport / Stimuli-sensing channels / plasma membrane
Similarity search - Function
Sodium leak channel NALCN / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / NALCN channel auxiliary factor 1 / Sodium leak channel NALCN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWu, J. / Yan, Z. / Ke, M.
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the human sodium leak channel NALCN in complex with FAM155A.
Authors: Jiongfang Xie / Meng Ke / Lizhen Xu / Shiyi Lin / Jin Huang / Jiabei Zhang / Fan Yang / Jianping Wu / Zhen Yan /
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 ...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 binding site in Ca 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, 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.
History
DepositionJul 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: Sodium leak channel non-selective protein
B: Transmembrane protein FAM155A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,57616
Polymers258,2212
Non-polymers9,35514
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17020 Å2
ΔGint-107 kcal/mol
Surface area70700 Å2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Sodium leak channel non-selective protein / CanIon / Voltage gated channel-like protein 1


Mass: 203616.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NALCN, VGCNL1 / Production host: Homo sapiens (human) / References: UniProt: Q8IZF0
#2: Protein Transmembrane protein FAM155A / Transmembrane protein


Mass: 54604.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM155A / Production host: Homo sapiens (human) / References: UniProt: B1AL88

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Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 10 molecules

#6: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY

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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: Binary complex of human NALCN with FAM155A / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65177 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612236
ELECTRON MICROSCOPYf_angle_d0.59816591
ELECTRON MICROSCOPYf_dihedral_angle_d27.1561585
ELECTRON MICROSCOPYf_chiral_restr0.0431870
ELECTRON MICROSCOPYf_plane_restr0.0042054

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