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- EMDB-25493: Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conf... -

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Basic information

Entry
Database: EMDB / ID: EMD-25493
TitleHuman NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conformation 2/2
Map datasharpened map used for model refinements
Sample
  • Complex: Pentameric complex of the leak channel NALCN with FAM155A, Calmodulin, UNC79 and UNC80
    • Protein or peptide: Sodium leak channel non-selective protein,Enhanced green fluorescent protein
    • Protein or peptide: Transmembrane protein FAM155A
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: UNC79,Protein unc-79 homolog
    • Protein or peptide: Protein unc-80 homolog
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordsion channel / calmodulin / HEAT repeat protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


monoatomic cation homeostasis / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / cation channel complex / CaM pathway / Cam-PDE 1 activation / voltage-gated sodium channel activity / Sodium/Calcium exchangers / sodium channel activity ...monoatomic cation homeostasis / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / cation channel complex / CaM pathway / Cam-PDE 1 activation / voltage-gated sodium channel activity / Sodium/Calcium exchangers / sodium channel activity / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / monoatomic ion channel complex / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / calcium ion import across plasma membrane / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / sodium ion transmembrane transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / monoatomic cation channel activity / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / potassium ion transmembrane transport / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / bioluminescence / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / generation of precursor metabolites and energy / spindle microtubule / positive regulation of synaptic transmission, GABAergic / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / calcium ion transmembrane transport / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / RAS processing
Similarity search - Function
UNC79 / Cation channel complex component UNC80, N-terminal / Protein UNC80, central region / Protein UNC80, C-terminal / Cation-channel complex subunit UNC-79 / UNC80 N-terminal / Protein UNC80 central region / Protein UNC80 C-terminal region / Sodium leak channel NALCN / : ...UNC79 / Cation channel complex component UNC80, N-terminal / Protein UNC80, central region / Protein UNC80, C-terminal / Cation-channel complex subunit UNC-79 / UNC80 N-terminal / Protein UNC80 central region / Protein UNC80 C-terminal region / Sodium leak channel NALCN / : / Voltage-dependent channel domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Armadillo-type fold
Similarity search - Domain/homology
Enhanced green fluorescent protein / NALCN channel auxiliary factor 1 / Calmodulin-1 / Sodium leak channel NALCN / Protein unc-80 homolog / Protein unc-79 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKschonsak M / Chua HC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structural architecture of the human NALCN channelosome.
Authors: Marc Kschonsak / Han Chow Chua / Claudia Weidling / Nourdine Chakouri / Cameron L Noland / Katharina Schott / Timothy Chang / Christine Tam / Nidhi Patel / Christopher P Arthur / Alexander ...Authors: Marc Kschonsak / Han Chow Chua / Claudia Weidling / Nourdine Chakouri / Cameron L Noland / Katharina Schott / Timothy Chang / Christine Tam / Nidhi Patel / Christopher P Arthur / Alexander Leitner / Manu Ben-Johny / Claudio Ciferri / Stephan Alexander Pless / Jian Payandeh /
Abstract: Depolarizing sodium (Na) leak currents carried by the NALCN channel regulate the resting membrane potential of many neurons to modulate respiration, circadian rhythm, locomotion and pain sensitivity. ...Depolarizing sodium (Na) leak currents carried by the NALCN channel regulate the resting membrane potential of many neurons to modulate respiration, circadian rhythm, locomotion and pain sensitivity. NALCN requires FAM155A, UNC79 and UNC80 to function, but the role of these auxiliary subunits is not understood. NALCN, UNC79 and UNC80 are essential in rodents, and mutations in human NALCN and UNC80 cause severe developmental and neurological disease. Here we determined the structure of the NALCN channelosome, an approximately 1-MDa complex, as fundamental aspects about the composition, assembly and gating of this channelosome remain obscure. UNC79 and UNC80 are massive HEAT-repeat proteins that form an intertwined anti-parallel superhelical assembly, which docks intracellularly onto the NALCN-FAM155A pore-forming subcomplex. Calmodulin copurifies bound to the carboxy-terminal domain of NALCN, identifying this region as a putative modulatory hub. Single-channel analyses uncovered a low open probability for the wild-type complex, highlighting the tightly closed S6 gate in the structure, and providing a basis to interpret the altered gating properties of disease-causing variants. Key constraints between the UNC79-UNC80 subcomplex and the NALCN DI-DII and DII-DIII linkers were identified, leading to a model of channelosome gating. Our results provide a structural blueprint to understand the physiology of the NALCN channelosome and a template for drug discovery to modulate the resting membrane potential.
History
DepositionNov 22, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7sx4
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25493.png

Downloads & links

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Map

FileDownload / File: emd_25493.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map used for model refinements
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 400 pix.
= 469.28 Å		1.17 Å/pix.
x 400 pix.
= 469.28 Å		1.17 Å/pix.
x 400 pix.
= 469.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 8.0 / Movie #1: 8
Minimum - Maximum-32.627827000000003 - 43.383907000000001
Average (Standard dev.)-0.04411089 (±2.2761886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 469.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.17321.17321.1732
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z469.280469.280469.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-32.62843.384-0.044

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Supplemental data

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Additional map: map (non-sharpened) of overall NALCN-FAM-UNC79-UNC80-CAM

Fileemd_25493_additional_1.map
Annotationmap (non-sharpened) of overall NALCN-FAM-UNC79-UNC80-CAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pentameric complex of the leak channel NALCN with FAM155A, Calmod...

EntireName: Pentameric complex of the leak channel NALCN with FAM155A, Calmodulin, UNC79 and UNC80
Components
  • Complex: Pentameric complex of the leak channel NALCN with FAM155A, Calmodulin, UNC79 and UNC80
    • Protein or peptide: Sodium leak channel non-selective protein,Enhanced green fluorescent protein
    • Protein or peptide: Transmembrane protein FAM155A
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: UNC79,Protein unc-79 homolog
    • Protein or peptide: Protein unc-80 homolog
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Pentameric complex of the leak channel NALCN with FAM155A, Calmod...

SupramoleculeName: Pentameric complex of the leak channel NALCN with FAM155A, Calmodulin, UNC79 and UNC80
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Calmodulin was not overexpressed but co-purified from Expi293 cells
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium leak channel non-selective protein,Enhanced green fluoresc...

MacromoleculeName: Sodium leak channel non-selective protein,Enhanced green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 234.128797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLKRKQSSRV EAQPVTDFGP DESLSDNADI LWINKPWVHS LLRICAIISV ISVCMNTPMT FEHYPPLQYV TFTLDTLLMF LYTAEMIAK MHIRGIVKGD SSYVKDRWCV FDGFMVFCLW VSLVLQVFEI ADIVDQMSPW GMLRIPRPLI MIRAFRIYFR F ELPRTRIT ...String:
MLKRKQSSRV EAQPVTDFGP DESLSDNADI LWINKPWVHS LLRICAIISV ISVCMNTPMT FEHYPPLQYV TFTLDTLLMF LYTAEMIAK MHIRGIVKGD SSYVKDRWCV FDGFMVFCLW VSLVLQVFEI ADIVDQMSPW GMLRIPRPLI MIRAFRIYFR F ELPRTRIT NILKRSGEQI WSVSIFLLFF LLLYGILGVQ MFGTFTYHCV VNDTKPGNVT WNSLAIPDTH CSPELEEGYQ CP PGFKCMD LEDLGLSRQE LGYSGFNEIG TSIFTVYEAA SQEGWVFLM(TYS) RAIDSFPRWR SYFYFITLIF FLAWLVKNV FIAVIIETFA EIRVQFQQMW GSRSSTTSTA TTQMFHEDAA GGWQLVAVDV NKPQGRAPAC LQKMMRSSVF HMFILSMVTV DVIVAASNY YKGENFRRQY DEFYLAEVAF TVLFDLEALL KIWCLGFTGY ISSSLHKFEL LLVIGTTLHV YPDLYHSQFT Y FQVLRVVR LIKISPALED FVYKIFGPGK KLGSLVVFTA SLLIVMSAIS LQMFCFVEEL DRFTTFPRAF MSMFQILTQE GW VDVMDQT LNAVGHMWAP VVAIYFILYH LFATLILLSL FVAVILDNLE LDEDLKKLKQ LKQSEANADT KEKLPLRLRI FEK FPNRPQ MVKISKLPSD FTVPKIRESF MKQFIDRQQQ DTCCLLRSLP TTSSSSCDHS KRSAIEDNKY IDQKLRKSVF SIRA RNLLE KETAVTKILR ACTRQRMLSG SFEGQPAKER SILSVQHHIR QERRSLRHGS NSQRISRGKS LETLTQDHSN TVRYR NAQR EDSEIKMIQE KKEQAEMKRK VQEEELRENH PYFDKPLFIV GREHRFRNFC RVVVRARFNA SKTDPVTGAV KNTKYH QLY DLLGLVTYLD WVMIIVTICS CISMMFESPF RRVMHAPTLQ IAEYVFVIFM SIELNLKIMA DGLFFTPTAV IRDFGGV MD IFIYLVSLIF LCWMPQNVPA ESGAQLLMVL RCLRPLRIFK LVPQMRKVVR ELFSGFKEIF LVSILLLTLM LVFASFGV Q LFAGKLAKCN DPNIIRREDC NGIFRINVSV SKNLNLKLRP GEKKPGFWVP RVWANPRNFN FDNVGNAMLA LFEVLSLKG WVEVRDVIIH RVGPIHGIYI HVFVFLGCMI GLTLFVGVVI ANFNENKGTA LLTVDQRRWE DLKSRLKIAQ PLHLPPRPDN DGFRAKMYD ITQHPFFKRT IALLVLAQSV LLSVKWDVED PVTVPLATMS VVFTFIFVLE VTMKIIAMSP AGFWQSRRNR Y DLLVTSLG VVWVVLHFAL LNAYTYMMGA CVIVFRFFSI CGKHVTLKML LLTVVVSMYK SFFIIVGMFL LLLCYAFAGV VL FGTVKYG ENINRHANFS SAGKAITVLF RIVTGEDWNK IMHDCMVQPP FCTPDEFTYW ATDCGNYAGA LMYFCSFYVI IAY IMLNLL VAIIVENFSL FYSTEEDQLL SYNDLRHFQI IWNMVDDKRE GVIPTFRVKF LLRLLRGRLE VDLDKDKLLF KHMC YEMER LHNGGDVTFH DVLSMLSYRS VDIRKSLQLE ELLAREQLEY TIEEEVAKQT IRMWLKKCLK RIRAKQQQSC SIIHS LRES QQQELSRFLN PPSIETTQPS EDTNANSQDN SMQPETSSQQ QLLSPTLSDR GGSRQDAADA GKPQRKFGQW RLPSAP KPI SHSVSSVNLR FGGRTTMKSV VCKMNPMTDA ASCGSEVKKW WTRQLTVESD ESGDDLLDIG GSLVPRGSSG ENLYFQG SS GMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPD H MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS HNVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSK LSKDPNEKRD HMVLLEFVTA AGITLGMDEL YKSGGDYKD DDDKGSGSAW SHPQFEKGGG SGGGSGGSAW SHPQFEK

UniProtKB: Sodium leak channel NALCN, Enhanced green fluorescent protein

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Macromolecule #2: Transmembrane protein FAM155A

MacromoleculeName: Transmembrane protein FAM155A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.205004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTRGAWMCRQ YDDGLKIWLA APRENEKPFI DSERAQKWRL SLASLLFFTV LLSDHLWFCA EAKLTRARDK EHQQQQRQQQ QQQQQQRQR QQQQQQRRQQ EPSWPALLAS MGESSPAAQA HRLLSASSSP TLPPSPGDGG GGGGKGNRGK DDRGKALFLG N SAKPVWRL ...String:
MTRGAWMCRQ YDDGLKIWLA APRENEKPFI DSERAQKWRL SLASLLFFTV LLSDHLWFCA EAKLTRARDK EHQQQQRQQQ QQQQQQRQR QQQQQQRRQQ EPSWPALLAS MGESSPAAQA HRLLSASSSP TLPPSPGDGG GGGGKGNRGK DDRGKALFLG N SAKPVWRL ETCYPQGASS GQCFTVENAD AVCARNWSRG AAGGDGQEVR SKHPTPLWNL SDFYLSFCNS YTLWELFSGL SS PNTLNCS LDVVLKEGGE MTTCRQCVEA YQDYDHHAQE KYEEFESVLH KYLQSEEYSV KSCPEDCKIV YKAWLCSQYF EVT QFNCRK TIPCKQYCLE VQTRCPFILP DNDEVIYGGL SSFICTGLYE TFLTNDEPEC CDVRREEKSN NPSKGTVEKS GSCH RTSLT VSSATRLCNS RLKLCVLVLI LLHTVLTASA AQNTAGLSFG GINTLEENST NEEGGSGGSD YKDDDDKGNS DYKDD DDK

UniProtKB: NALCN channel auxiliary factor 1

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Macromolecule #3: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #4: UNC79,Protein unc-79 homolog

MacromoleculeName: UNC79,Protein unc-79 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 285.174938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)LP YTMISTLATF PPFLHKDIIE YLSTSFLP M AILGSSRREG VPAHVNLSAS SMLMIAMQYT SNPVYHCQLL ECLMKYKQEV WKDLLYVIAY GPSQVKPPAV QMLFHYWPN LKPPGAISEY RGLQYTAWNP IHCQHIECHN AINKPAVKMC IDPSLSVALG DKPPPLYLCE ECSERIAGDH SEWLIDVLLP QAEISAICQ KKNCSSHVRR AVVTCFSAGC CGRHGNRPVR YCKRCHSNHH SNEVGAAAET HLYQTSPPPI NTRECGAEEL V CAVEAVIS LLKEAEFHAE QREHELNRRR QLGLSSSHHS LDNADFDNKD DDKHDQRLLS QFGIWFLVSL CTPSENTPTE SL ARLVAMV FQWFHSTAYM MDDEVGSLVE KLKPQFVTKW LKTVCDVRFD VMVMCLLPKP MEFARVGGYW DKSCSTVTQL KEG LNRILC LIPYNVINQS VWECIMPEWL EAIRTEVPDN QLKEFREVLS KMFDIELCPL PFSMEEMFGF ISCRFTGYPS SVQE QALLW LHVLSELDIM VPLQLLISMF SDGVNSVKEL ANQRKSRVSE LAGNLASRRV SVASDPGRRV QHNMLSPFHS PFQSP FRSP LRSPFRSPFK NFGHPGGRTI DFDCEDDEMN LNCFILMFDL LLKQMELQDD GITMGLEHSL SKDIISIINN VFQAPW GGS HTCQKDEKAI ECNLCQSSIL CYQLACELLE RLAPKEESRL VEPTDSLEDS LLSSRPEFII GPEGEEEENP ASKHGEN PG NCTEPVEHAA VKNDTERKFC YQQLPVTLRL IYTIFQEMAK FEEPDILFNM LNCLKILCLH GECLYIARKD HPQFLAYI Q DHMLIASLWR VVKSEFSQLS SLAVPLLLHA LSLPHGADIF WTIINGNFNS KDWKMRFEAV EKVAVICRFL DIHSVTKNH LLKYSLAHAF CCFLTAVEDV NPAVATRAGL LLDTIKRPAL QGLCLCLDFQ FDTVVKDRPT ILSKLLLLHF LKQDIPALSW EFFVNRFET LSLEAQLHLD CNKEFPFPTT ITAVRTNVAN LSDAALWKIK RARFARNRQK SVRSLRDSVK GPVESKRALS L PETLTSKI RQQSPENDNT IKDLLPEDAG IDHQTVHQLI TVLMKFMAKD ESSAESDISS AKAFNTVKRH LYVLLGYDQQ EG CFMIAPQ KMRLSTCFNA FIAGIAQVMD YNINLGKHLL PLVVQVLKYC SCPQLRHYFQ QPPRCSLWSL KPHIRQMWLK ALL VILYKY PYRDCDISKI LLHLIHITVN TLNAQYHSCK PHATAGPLYS DNSNISRYSE KEKGEIELAE YRETGALQDS LLHC VREES IPKKKLRSFK QKSLDIGNAD SLLFTLDEHR RKSCIDRCDI EKPPTQAAYI AQRPNDPGRS RQNSATRPDN SEIPE NPAM EGFPDARRPV IPEVRLNCME TFEVKVDSPV KPAPKEDLDL IDLSSDSTSG PEKHSILSTS DSDSLVFEPL PPLRIV ESD EEEETMNQGD DGPSGKNAAS SPSVPSHPSV LSLSTAPLVQ VSVEDCSKDF SSKDSGNNQS AGNTDSALIT LEDPMDA EG SSKPEELPEF SCGSPLTLKQ KRDLLQKSFA LPEMSLDDHP DPGTEGEKPG ELMPSSGAKT VLLKVPEDAE NPTESEKP D TSAESDTEQN PERKVEEDGA EESEFKIQIV PRQRKQRKIA VSAIQREYLD ISFNILDKLG EQKDPDPSTK GLSTLEMPR ESSSAPTLDA GVPETSSHSS ISTQYRQMKR GSLGVLTMSQ LMKRQLEHQS SAPHNISNWD TEQIQPGKRQ CNVPTCLNPD LEGQPLRMR GATKSSLLSA PSIVSMFVPA PEEFTDEQPT VMTDKCHDCG AILEEYDEET LGLAIVVLST FIHLSPDLAA P LLLDIMQS VGRLASSTTF SNQAESMMVP GNAAGVAKQF LRCIFHQLAP NGIFPQLFQS TIKDGTFLRT LASSLMDFNE LS SIAALSQ LLEGLNNKKN LPAGGAMIRC LENIATFMEA LPMDSPSSLW TTISNQFQTF FAKLPCVLPL KCSLDSSLRI MIC LLKIPS TNATRSLLEP FSKLLSFVIQ NAVFTLAYLV ELCGLCYRAF TKERDKFYLS RSVVLELLQA LKLKSPLPDT NLLL LVQFI CADAGTKLAE STILSKQMIA SVPGCGTAAM ECVRQYINEV LDFMADMHTL TKLKSHMKTC SQPLHEDTFG GHLKV GLAQ IAAMDISRGN HRDNKAVIRY LPWLYHPPSA MQQGPKEFIE CVSHIRLLSW LLLGSLTHNA VCPNASSPCL PIPLDA GSH VADHLIVILI GFPEQSKTSV LHMCSLFHAF IFAQLWTVYC EQSAVATNLQ NQNEFSFTAI LTALEFWSRV TPSILQL MA HNKVMVEMVC LHVISLMEAL QECNSTIFVK LIPMWLPMIQ SNIKHLSAGL QLRLQAIQNH VNHHSLRTLP GSGQSSAG L AALRKWLQCT QFKMAQVEIQ SSEAASQFYP LGGSGGSDYK DDDDKGNSDY KDDDDK

UniProtKB: Protein unc-79 homolog

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Macromolecule #5: Protein unc-80 homolog

MacromoleculeName: Protein unc-80 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 366.510594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVKRKSSEGQ EQDGGRGIPL PIQTFLWRQT SAFLRPKLGK QYEASCVSFE RVLVENKLHG LSPALSEAIQ SISRWELVQA ALPHVLHCT ATLLSNRNKL GHQDKLGVAE TKLLHTLHWM LLEAPQDCNN ERFGGTDRGS SWGGSSSAFI HQVENQGSPG Q PCQSSSND ...String:
MVKRKSSEGQ EQDGGRGIPL PIQTFLWRQT SAFLRPKLGK QYEASCVSFE RVLVENKLHG LSPALSEAIQ SISRWELVQA ALPHVLHCT ATLLSNRNKL GHQDKLGVAE TKLLHTLHWM LLEAPQDCNN ERFGGTDRGS SWGGSSSAFI HQVENQGSPG Q PCQSSSND EEENNRRKIF QNSMATVELF VFLFAPLVHR IKESDLTFRL ASGLVIWQPM WEHRQPGVSG FTALVKPIRN II TAKRSSP INSQSRTCES PNQDARHLEG LQVVCETFQS DSISPKATIS GCHRGNSFDG SLSSQTSQER GPSHSRASLV IPP CQRSRY ATYFDVAVLR CLLQPHWSEE GTQWSLMYYL QRLRHMLEEK PEKPPEPDIP LLPRPRSSSM VAAAPSLVNT HKTQ DLTMK CNEEEKSLSS EAFSKVSLTN LRRSAVPDLS SDLGMNIFKK FKSRKEDRER KGSIPFHHTG KRRPRRMGVP FLLHE DHLD VSPTRSTFSF GSFSGLGEDR RGIEKGGWQT TILGKLTRRG SSDAATEMES LSARHSHSHH TLVSDLPDPS NSHGEN TVK EVRSQISTIT VATFNTTLAS FNVGYADFFN EHMRKLCNQV PIPEMPHEPL ACANLPRSLT DSCINYSYLE DTEHIDG TN NFVHKNGMLD LSVVLKAVYL VLNHDISSRI CDVALNIVEC LLQLGVVPCV EKNRKKSENK ENETLEKRPS EGAFQFKG V SGSSTCGFGG PAVSGAGDGG GEEGGGGDGG GGGGDGGGGG GGGGGPYEKN DKNQEKDEST PVSNHRLALT MLIKIVKSL GCAYGCGEGH RGLSGDRLRH QVFRENAQNC LTKLYKLDKM QFRQTMRDYV NKDSLNNVVD FLHALLGFCM EPVTDNKAGF GNNFTTVDN KSTAQNVEGI IVSAMFKSLI TRCASTTHEL HSPENLGLYC DIRQLVQFIK EAHGNVFRRV ALSALLDSAE K LAPGKKVE ENEQESKPAG SKRSEAGSIV DKGQVSSAPE ECRSFMSGRP SQTPEHDEQM QGANLGRKDF WRKMFKSQSA AS DTSSQSE QDTSECTTAH SGTTSDRRAR SRSRRISLRK KLKLPIGKRN WLKRSSLSGL ADGVEDLLDI SSVDRLSFIR QSS KVKFTS AVKLSEGGPG SGMENGRDEE ENFFKRLGCH SFDDHLSPNQ DGGKSKNVVN LGAIRQGMKR FQFLLNCCEP GTIP DASIL AAALDLEAPV VARAALFLEC ARFVHRCNRG NWPEWMKGHH VNITKKGLSR GRSPIVGNKR NQKLQWNAAK LFYQW GDAI GVRLNELCHG ESESPANLLG LIYDEETKRR LRKEDEEEDF LDDSTVNPSK CGCPFALKMA ACQLLLEITT FLRETF SCL PRPRTEPLVD LESCRLRLDP ELDRHRYERK ISFAGVLDEN EDSKDSLHSS SHTLKSDAGV EEKKEGSPWS ASEPSIE PE GMSNAGAEEN YHRNMSWLHV MILLCNQQSF ICTHVDYCHP HCYLHHSRSC ARLVRAIKLL YGDSVDSLRE SSNISSVA L RGKKQKECSD KSCLRTPSLK KRVSDANLEG KKDSGMLKYI RLQVMSLSPA PLSLLIKAAP ILTEEMYGDI QPAAWELLL SMDEHMAGAA AAMFLLCAVK VPEAVSDMLM SEFHHPETVQ RLNAVLKFHT LWRFRYQVWP RMEEGAQQIF KIPPPSINFT LPSPVLGMP SVPMFDPPWV PQCSGSVQDP INEDQSKSFS ARAVSRSHQR AEHILKNLQQ EEEKKRLGRE ASLITAIPIT Q EACYEPTC TPNSEPEEEV EEVTNLASRR LSVSPSCTSS TSHRNYSFRR GSVWSVRSAV SAEDEEHTTE HTPNHHVPQP PQ AVFPACI CAAVLPIVHL MEDGEVREDG VAVSAVAQQV LWNCLIEDPS TVLRHFLEKL TISNRQDELM YMLRKLLLNI GDF PAQTSH ILFNYLVGLI MYFVRTPCEW GMDAISATLT FLWEVVGYVE GLFFKDLKQT MKKEQCEVKL LVTASMPGTK TLVV HGQNE CDIPTQLPVH EDTQFEALLK ECLEFFNIPE SQSTHYFLMD KRWNLIHYNK TYVRDIYPFR RSVSPQLNLV HMHPE KGQE LIQKQVFTRK LEEVGRVLFL ISLTQKIPTA HKQSHVSMLQ EDLLRLPSFP RSAIDAEFSL FSDPQAGKEL FGLDTL QKS LWIQLLEEMF LGMPSEFPWG DEIMLFLNVF NGALILHPED SALLRQYAAT VINTAVHFNH LFSLSGYQWI LPTMLQV YS DYESNPQLRQ AIEFACHQFY ILHRKPFVLQ LFASVAPLLE FPDAANNGPS KGVSAQCLFD LLQSLEGETT DILDILEL V KAEKPLKSLD FCYGNEDLTF SISEAIKLCV TVVAYAPESF RSLQMLMVLE ALVPCYLQKL KRQTSQVETV PAAREEIAA TAALATSLQA LLYSVEVLTR PMTAPQMSRC DQGHKGTTTA NHTMSSGVNT RYQEQGAKLH FIRENLHLLE EGQGIPREEL DERIAREEF RRPRESLLNI CTEFYKHCGP RLKILQNLAG EPRVIALELL DVKSHMRLAE IAHSLLKLAP YDTQTMESRG L RRYIMEML PITDWTAEAV RPALILILKR LDRMFNKIHK MPTLRRQVEW EPASNLIEGV CLTLQRQPII SFLPHLRSLI NV CVNLVMG VVGPSSVADG LPLLHLSPYL SPPLPFSTAV VRLVALQIQA LKEDFPLSHV ISPFTNQERR EGMLLNLLIP FVL TVGSGS KDSPWLEQPE VQLLLQTVIN VLLPPRIIST SRSKNFMLES SPAHCSTPGD AGKDLRREGL AESTSQAAYL ALKV ILVCF ERQLGSQWYW LSLQVKEMAL RKVGGLALWD FLDFIVRTRI PIFVLLRPFI QCKLLAQPAE NHEELSARQH IADQL ERRF IPRPLCKSSL IAEFNSELKI LKEAVHSGSA YQGKTSISTV GTSTSAYRLS LATMSRSNTG TGTVWEQDSE PSQQAS QDT LSRTDEEDEE NDSISMPSVV SEQEAYLLSA IGRRRFSSHV SSMSVPQAEV GMLPSQSEPN VLDDSQGLAA EGSLSRV AS IQSEPGQQNL LVQQPLGRKR GLRQLRRPLL SRQKTQTEPR NRQGARLSTT RRSIQPKTKP SADQKRSVTF IEAQPEPA A APTDALPATG QLQGCSPAPS RKPEAMDEPV LTSSPAIVVA DLHSVSPKQS ENFPTEEGEK EEDTEAQGAT AHSPLSAQL SDPDDFTGLE TSSLLQHGDT VLHISEENGM ENPLLSSQFT FTPTELGKTD AVLDESHVGG SGGSDYKDDD DKGNSDYKDD DDK

UniProtKB: Protein unc-80 homolog

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 7 / Number of copies: 1 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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Macromolecule #8: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 8 / Number of copies: 1 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Macromolecule #9: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.65 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
25.0 mMHEPES
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: 3.5 sec blotting.
DetailsNALCN was reconstituted into lipid nanodiscs and mildly crosslinkned with 0.05% EM grade glutaraldehyde for 10 min at room temperature. Cross-linking was quenched with 9 mM Tris pH 7.5

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 26550 / Average exposure time: 3.0 sec. / Average electron dose: 64.009 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3048401
Startup modelType of model: OTHER / Details: ab initio 3D reconstruction within cisTEM
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02) / Number images used: 56037
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM (ver. 1.02)
Final angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.02) / Details: manual refine in cisTEM of a single class
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1)

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