[English] 日本語
Yorodumi
- EMDB-30470: Structure of mammalian NALCN-FAM155A complex at 2.65 angstrom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30470
TitleStructure of mammalian NALCN-FAM155A complex at 2.65 angstrom
Map datamap after postprocessing
Sample
  • Complex: NALCN-FAM155A complex
    • Protein or peptide: Sodium leak channel non-selective protein
    • Protein or peptide: Transmembrane protein FAM155A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: CHOLESTEROL
Function / homology
Function and homology information


positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / voltage-gated sodium channel activity / sodium ion transmembrane transport / calcium ion import across plasma membrane / monoatomic cation channel activity / potassium ion transmembrane transport ...positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / voltage-gated sodium channel activity / sodium ion transmembrane transport / calcium ion import across plasma membrane / monoatomic cation channel activity / potassium ion transmembrane transport / positive regulation of synaptic transmission, GABAergic / calcium ion transmembrane transport / plasma membrane
Similarity search - Function
NALCN channel auxiliary factor 1/2 / Sodium leak channel NALCN / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium leak channel NALCN / NALCN channel auxiliary factor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsChen L / Kang Y
Funding support China, 5 items
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, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7cu3
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30470.png

Downloads & links

-
Map

FileDownload / File: emd_30470.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap after postprocessing
Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.12012658 - 0.2167746
Average (Standard dev.)-0.00013046713 (±0.009890032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 250.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z250.800250.800250.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1200.217-0.000

-
Supplemental data

-
Sample components

-
Entire : NALCN-FAM155A complex

EntireName: NALCN-FAM155A complex
Components
  • Complex: NALCN-FAM155A complex
    • Protein or peptide: Sodium leak channel non-selective protein
    • Protein or peptide: Transmembrane protein FAM155A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: CHOLESTEROL

-
Supramolecule #1: NALCN-FAM155A complex

SupramoleculeName: NALCN-FAM155A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Sodium leak channel non-selective protein

MacromoleculeName: Sodium leak channel non-selective protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 200.682031 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 TSIFTVYEAS SQEGWVFLMY RAIDSFPRWR SYFYFITLIF FLAWLVKNVF IAV IIETFA EIRVQFQQMW GTRSSTTSTA TTQMFHEDAA GGWQLVAVDV NKPQGRAPAC LQKMMRSSVF HMFILSMVTV DVIV AASNY YKGENFRRQY DEFYLAEVAF TVLFDLEALL KIWCLGFTGY ISSSLHKFEL LLVIGTTLHV YPDLYHSQFT YFQVL RVVR LIKISPALED FVYKIFGPGK KLGSLVVFTA SLLIVMSAIS LQMFCFVEEL DRFTTFPRAF MSMFQILTQE GWVDVM DQT LNAVGHMWAP LVAIYFILYH LFATLILLSL FVAVILDNLE LDEDLKKLKQ LKQSEANADT KEKLPLRLRI FEKFPNR PQ MVKISKLPSD FTVPKIRESF MKQFIDRQQQ DTCCLFRILP STSSSSCDNP KRPTVEDNKY IDQKLRKSVF SIRARNLL E KETAVTKILR ACTRQRMLSG SFEGQPAKER SILSVQHHIR QERRSLRHGS NSQRISRGKS LETLTQDHSN TVRYRNAQR EDSEIKMIQE KKEQAEMKRK VQEEELRENH PYFDKPLFIV GREHRFRNFC RVVVRARFNA SKTDPVTGAV KNTKYHQLYD LLGLVTYLD WVMITVTICS CISMMFESPF RRVMHAPTLQ IAEYVFVIFM SIELNLKIMA DGLFFTPTAV IRDFGGVMDI F IYLVSLIF LCWMPQNVPA ESGAQLLMVL RCLRPLRIFK LVPQMRKVVR ELFSGFKEIF LVSILLLTLM LVFASFGVQL FA GKLAKCN DPNIIRREDC NGIFRINVSV SKNLNLKLRP GEKKPGFWVP RVWANPRNFN FDNVGNAMLA LFEVLSLKGW VEV RDVIIH RVGPIHGIYI HVFVFLGCMI GLTLFVGVVI ANFNENKGTA LLTVDQRRWE DLKSRLKIAQ PLHLPPRPDN DGFR AKMYD ITQHPFFKRT IALLVLAQSV LLSVKWDVED PVTVPLATMS VVFTFIFVLE VTMKIIAMSP AGFWQSRRNR YDLLV TSLG VVWVVLHFAL LNAYTYMMGA CVIVFRFFSI CGKHVTLKML LLTVVVSMYK SFFIIVGMFL LLLCYAFAGV VLFGTV KYG ENINRHANFS SAGKAITVLF RIVTGEDWNK IMHDCMVQPP FCTPDEFTYW ATDCGNYAGA LMYFCSFYVI IAYIMLN LL VAIIVENFSL FYSTEEDQLL SYNDLRHFQI IWNMVDDKRE GVIPTFRVKF LLRLLRGRLE VDLDKDKLLF KHMCYEME R LHNGGDVTFH DVLSMLSYRS VDIRKSLQLE ELLAREQLEY TIEEEVAKQT IRMWLKKCLK RIRAKQQQSC SIIHSLRES QQQELSRFLN PPSIETTQPS EDTNANSQDH NTQPESSSQQ QLLSPTLSDR GGSRQDAADT GKPQRKIGQW RLPSAPKPIS HSVSSVNLR FGGRTTMKSV VCKMNPMPDT ASCGSEVKKW WTRQLTVESD ESGDDLLDI

-
Macromolecule #2: Transmembrane protein FAM155A

MacromoleculeName: Transmembrane protein FAM155A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.795801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTRGAWMCRQ YDDGLKIWLA APRENEKPFI DSERAQKWRL SLASLLFFTV LLSDHLWFCA EAKLTRTRDK EHHQQQQQQQ QQQQQQQQQ QQQQQQRQQQ RQRQQQRQRQ QEPSWPALLA SMGESSPAAQ AHRLLSASSS PTLPPSPGGG GGSKGNRGKN N RSRALFLG ...String:
MTRGAWMCRQ YDDGLKIWLA APRENEKPFI DSERAQKWRL SLASLLFFTV LLSDHLWFCA EAKLTRTRDK EHHQQQQQQQ QQQQQQQQQ QQQQQQRQQQ RQRQQQRQRQ QEPSWPALLA SMGESSPAAQ AHRLLSASSS PTLPPSPGGG GGSKGNRGKN N RSRALFLG NSAKPVWRLE TCYPQGASSG QCFTVESADA VCARNWSRGA AAGEEQSSRG SRPTPLWNLS DFYLSFCNSY TL WELFSGL SSPSTLNCSL DVVLTEGGEM TTCRQCIEAY QDYDHHAQEK YEEFESVLHK YLQSDEYSVK SCPEDCKIVY KAW LCSQYF EVTQFNCRKT IPCKQYCLEV QTRCPFILPD NDEVIYGGLS SFICTGLYET FLTNDEPECC DIRSEEQTAP RPKG TVDRR DSCPRTSLTV SSATRLCPGR LKLCVLVLIL LHTVLTASAA QNSTGLGLGG LPTLEDNSTR ED

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #4: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 12 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

-
Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 135043
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more