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- PDB-7cu3: Structure of mammalian NALCN-FAM155A complex at 2.65 angstrom -

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Basic information

Entry
Database: PDB / ID: 7cu3
TitleStructure of mammalian NALCN-FAM155A complex at 2.65 angstrom
Components
  • Sodium leak channel non-selective protein
  • Transmembrane protein FAM155A
KeywordsTRANSPORT PROTEIN / NALCN / Channel / FAM155 / NCA / NLF
Function / homology
Function and homology information


Stimuli-sensing channels / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / voltage-gated sodium channel activity / monoatomic ion channel complex / monoatomic cation channel activity / potassium ion transmembrane transport / sodium ion transmembrane transport / positive regulation of synaptic transmission, GABAergic ...Stimuli-sensing channels / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / voltage-gated sodium channel activity / monoatomic ion channel complex / monoatomic cation channel activity / potassium ion transmembrane transport / sodium ion transmembrane transport / positive regulation of synaptic transmission, GABAergic / calcium ion transmembrane transport / plasma membrane
Similarity search - Function
Sodium leak channel NALCN / : / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Chem-6OU / CHOLESTEROL / Sodium leak channel NALCN / NALCN channel auxiliary factor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsChen, L. / Kang, Y.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0502004 China
National Natural Science Foundation of China (NSFC)31622021 China
National Natural Science Foundation of China (NSFC)91857000 China
National Natural Science Foundation of China (NSFC)31821091 China
National Natural Science Foundation of China (NSFC)31870833 China
CitationJournal: Nat Commun / Year: 2020
Title: Structure of voltage-modulated sodium-selective NALCN-FAM155A channel complex.
Authors: Yunlu Kang / Jing-Xiang Wu / Lei Chen /
Abstract: Resting membrane potential determines the excitability of the cell and is essential for the cellular electrical activities. The NALCN channel mediates sodium leak currents, which positively adjust ...Resting membrane potential determines the excitability of the cell and is essential for the cellular electrical activities. The NALCN channel mediates sodium leak currents, which positively adjust resting membrane potential towards depolarization. The NALCN channel is involved in several neurological processes and has been implicated in a spectrum of neurodevelopmental diseases. Here, we report the cryo-EM structure of rat NALCN and mouse FAM155A complex to 2.7 Å resolution. The structure reveals detailed interactions between NALCN and the extracellular cysteine-rich domain of FAM155A. We find that the non-canonical architecture of NALCN selectivity filter dictates its sodium selectivity and calcium block, and that the asymmetric arrangement of two functional voltage sensors confers the modulation by membrane potential. Moreover, mutations associated with human diseases map to the domain-domain interfaces or the pore domain of NALCN, intuitively suggesting their pathological mechanisms.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
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Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
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Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
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Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
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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)263,53119
Polymers253,4782
Non-polymers10,05317
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6770 Å2
ΔGint-22 kcal/mol
Surface area65560 Å2

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Components

#1: Protein Sodium leak channel non-selective protein / Four domain-type voltage-gated ion channel alpha-1 subunit / Rb21-channel / Voltage gated channel- ...Four domain-type voltage-gated ion channel alpha-1 subunit / Rb21-channel / Voltage gated channel-like protein 1


Mass: 200682.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nalcn, Nca, Rb21, Vgcnl1 / Production host: Homo sapiens (human) / References: UniProt: Q6Q760
#2: Protein Transmembrane protein FAM155A


Mass: 52795.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fam155a / Production host: Homo sapiens (human) / References: UniProt: Q8CCS2
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C39H76NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: NALCN-FAM155A complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc1_3777: / Classification: refinement
EM software
IDNameCategory
9PHENIXmodel refinement
13cisTEM3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135043 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612508
ELECTRON MICROSCOPYf_angle_d0.63616895
ELECTRON MICROSCOPYf_dihedral_angle_d20.8724599
ELECTRON MICROSCOPYf_chiral_restr0.0441909
ELECTRON MICROSCOPYf_plane_restr0.0052052

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