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- EMDB-22203: Cryo-EM structure of the sodium leak channel NALCN-FAM155A complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22203
TitleCryo-EM structure of the sodium leak channel NALCN-FAM155A complex
Map data
SampleNALCN in complex with FAM155A
  • Sodium leak channel non-selective protein
  • Transmembrane protein FAM155ATransmembrane protein
  • (ligand) x 5
Function / homology
Function and homology information


leak channel activity / regulation of resting membrane potential / calcium ion import across plasma membrane / sodium channel activity / voltage-gated ion channel activity / sodium ion transmembrane transport / potassium ion transmembrane transport / regulation of ion transmembrane transport / cation channel activity / calcium ion transmembrane transport ...leak channel activity / regulation of resting membrane potential / calcium ion import across plasma membrane / sodium channel activity / voltage-gated ion channel activity / sodium ion transmembrane transport / potassium ion transmembrane transport / regulation of ion transmembrane transport / cation channel activity / calcium ion transmembrane transport / ion transmembrane transport / go:0005623: / integral component of membrane / plasma membrane
Transmembrane protein FAM155 / Sodium leak channel non-selective protein / Voltage-dependent channel domain superfamily / Ion transport domain
Transmembrane protein FAM155A / Sodium leak channel non-selective protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKschonsak M / Chua HC / Noland CL / Weidling C / Clairfeuille T / Bahlke OO / Ameen AO / Li ZR / Arthur CP / Ciferri C / Pless SA / Payandeh J
CitationJournal: Nature / Year: 2020
Title: Structure of the human sodium leak channel NALCN.
Authors: Marc Kschonsak / Han Chow Chua / Cameron L Noland / Claudia Weidling / Thomas Clairfeuille / Oskar Ørts Bahlke / Aishat Oluwanifemi Ameen / Zhong Rong Li / Christopher P Arthur / Claudio ...Authors: Marc Kschonsak / Han Chow Chua / Cameron L Noland / Claudia Weidling / Thomas Clairfeuille / Oskar Ørts Bahlke / Aishat Oluwanifemi Ameen / Zhong Rong Li / Christopher P Arthur / Claudio Ciferri / Stephan Alexander Pless / Jian Payandeh /
Abstract: Persistently depolarizing sodium (Na) leak currents that enhance electrical excitability have been described for decades. The entity responsible for the major background Na conductance in neurons had ...Persistently depolarizing sodium (Na) leak currents that enhance electrical excitability have been described for decades. The entity responsible for the major background Na conductance in neurons had remained a mystery until characterization of NALCN (Na leak channel, non-selective). NALCN-mediated currents regulate neuronal excitability linked to respiration, locomotion and circadian rhythm. NALCN activity is under tight regulation and NALCN mutations cause severe neurological disorders and early death. 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 NALCN structure in complex with FAM155A (Family with sequence similarity 155, member A). 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. Clues to the modulation of NALCN activity are revealed by unusual voltage-sensor domains with asymmetric linkages to the pore. We discover a tightly closed pore gate where the vast majority of missense patient mutations cause gain-of-function phenotypes that cluster around the S6-gate and distinctive π-bulges. Our study provides a framework to demystify the physiology of NALCN and a foundation to discover treatments for NALCN channelopathies and other electrical disorders.
Validation ReportPDB-ID: 6xiw

SummaryFull reportAbout validation report
History
DepositionJun 22, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xiw
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22203.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å
0.82 Å/pix.
x 360 pix.
= 296.64 Å
0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.17
Minimum - Maximum-0.6131234 - 0.92917466
Average (Standard dev.)-0.0042198454 (±0.038623333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8240.8240.824
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.6130.929-0.004

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Supplemental data

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Additional map: non-sharpened map

Fileemd_22203_additional.map
Annotationnon-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire NALCN in complex with FAM155A

EntireName: NALCN in complex with FAM155A
Details: NALCN, FAM155A, UNC80 and UNC79 co-expressed and NALCN-FAM155A co-purified
Number of components: 8

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Component #1: protein, NALCN in complex with FAM155A

ProteinName: NALCN in complex with FAM155A
Details: NALCN, FAM155A, UNC80 and UNC79 co-expressed and NALCN-FAM155A co-purified
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #2: protein, Sodium leak channel non-selective protein

ProteinName: Sodium leak channel non-selective protein
Details: TYR287 modeled with sulfonation (TYS) as the EM density indicates a post-translational modification of this residue.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 206.341641 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Transmembrane protein FAM155A

ProteinName: Transmembrane protein FAM155ATransmembrane protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.205004 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALM...

LigandName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.720012 kDa

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Component #6: ligand, (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHOR...

LigandName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.749007 kDa

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Component #7: ligand, CHOLESTEROL HEMISUCCINATE

LigandName: CHOLESTEROL HEMISUCCINATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.486726 kDa

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Component #8: ligand, water

LigandName: water / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2.4 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 49.967 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 165000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 15080

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 365512
3D reconstructionSoftware: cisTEM / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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