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- EMDB-6698: Structure of a eukaryotic voltage-gated sodium channel at near at... -

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Basic information

Entry
Database: EMDB / ID: EMD-6698
TitleStructure of a eukaryotic voltage-gated sodium channel at near atomic resolution
Map dataoverall map
Sample
  • Organelle or cellular component: voltage-gated sodium channelSodium channel
    • Protein or peptide: Sodium channel protein
  • Ligand: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine
  • Ligand: BETA-D-MANNOSE
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
Similarity search - Function
Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein PaFPC1
Similarity search - Component
Biological speciesPeriplaneta americana (American cockroach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShen H / Zhou Q / Pan X / Li Z / Wu J / Yan N
Funding support China, 2 items
OrganizationGrant numberCountry
the Ministry of Science and Technology of China2015CB910101, 2016YFA0500402, 2014ZX09507003-006 China
the National Natural Science Foundation of Chinaprojects 31621092, 31630017, and 31611130036 China
CitationJournal: Science / Year: 2017
Title: Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.
Authors: Huaizong Shen / Qiang Zhou / Xiaojing Pan / Zhangqiang Li / Jianping Wu / Nieng Yan /
Abstract: Voltage-gated sodium (Na) channels are responsible for the initiation and propagation of action potentials. They are associated with a variety of channelopathies and are targeted by multiple ...Voltage-gated sodium (Na) channels are responsible for the initiation and propagation of action potentials. They are associated with a variety of channelopathies and are targeted by multiple pharmaceutical drugs and natural toxins. Here, we report the cryogenic electron microscopy structure of a putative Na channel from American cockroach (designated NaPaS) at 3.8 angstrom resolution. The voltage-sensing domains (VSDs) of the four repeats exhibit distinct conformations. The entrance to the asymmetric selectivity filter vestibule is guarded by heavily glycosylated and disulfide bond-stabilized extracellular loops. On the cytoplasmic side, a conserved amino-terminal domain is placed below VSD, and a carboxy-terminal domain binds to the III-IV linker. The structure of NaPaS establishes an important foundation for understanding function and disease mechanism of Na and related voltage-gated calcium channels.
History
DepositionJan 21, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMar 8, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5x0m
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6698.png

Downloads & links

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Map

FileDownload / File: emd_6698.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall map
Voxel sizeX=Y=Z: 1.29 Å
Density
Contour LevelBy AUTHOR: 0.0465 / Movie #1: 0.08
Minimum - Maximum-0.26366407 - 0.391851
Average (Standard dev.)0.00046030077 (±0.014029253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2640.3920.000

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Supplemental data

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Additional map: overall map with B factor of -300

Fileemd_6698_additional.map
Annotationoverall map with B factor of -300
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : voltage-gated sodium channel

EntireName: voltage-gated sodium channelSodium channel
Components
  • Organelle or cellular component: voltage-gated sodium channelSodium channel
    • Protein or peptide: Sodium channel protein
  • Ligand: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine
  • Ligand: BETA-D-MANNOSE

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Supramolecule #1: voltage-gated sodium channel

SupramoleculeName: voltage-gated sodium channel / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Periplaneta americana (American cockroach)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Sodium channel protein

MacromoleculeName: Sodium channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Periplaneta americana (American cockroach)
Molecular weightTheoretical: 183.875422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMADNSPL IREERQRLFR PYTRAMLTAP SAQPAKENGK TEENKDNSR DKGRGANKDR DGSAHPDQAL EQGSRLPARM RNIFPAELAS TPLEDFDPFY KNKKTFVVVT KAGDIFRFSG E KSLWMLDP ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMADNSPL IREERQRLFR PYTRAMLTAP SAQPAKENGK TEENKDNSR DKGRGANKDR DGSAHPDQAL EQGSRLPARM RNIFPAELAS TPLEDFDPFY KNKKTFVVVT KAGDIFRFSG E KSLWMLDP FTPIRRVAIS TMVQPIFSYF IMITILIHCI FMIMPATQTT YILELVFLSI YTIEVVVKVL ARGFILHPFA YL RDPWNWL DFLVTLIGYI TLVVDLGHLY ALRAFRVLRS WRTVTIVPGW RTIVDALSLS ITSLKDLVLL LLFSLFVFAV LGL QIYMGV LTQKCVKHFP ADGSWGNFTD ERWFNYTSNS SHWYIPDDWI EYPLCGNSSG AGMCPPGYTC LQGYGGNPNY GYTS FDTFG WAFLSVFRLV TLDYWEDLYQ LALRSAGPWH ILFFIIVVFY GTFCFLNFIL AVVVMSYTHM VKRADEEKAA ERELK KEKK AASVANNTAN GQEQTTIEMN GDEAVVIDNN DQAARQQSDP ETPAPSVTQR LTDFLCVWDC CVPWQKLQGA IGAVVL SPF FELFIAVIIV LNITFMALDH HDMNIEFERI LRTGNYIFTS IYIVEAVLKI IALSPKFYFK DSWNVFDFII VVFAILE LG LEGVQGLSVF RSFRLLRVFR LAKFWPTLNN FMSVMTKSYG AFVNVMYVMF LLLFIFAIIG MQLFGMNYID NMERFPDG D LPRWNFTDFL HSFMIVFRAL CGEWIESMWD CMLVGDWSCI PFFVAVFFVG NLVILNLLIA LLLNNYGSFC TSPTSDEED SKDEDALAQI VRIFKRFKPN LNAVKLSPMK PDSEDIVESQ EIQGNNIADA EDVLAGEFPP DCCCNAFYKC FPSRPARDSS VQRMWSNIR RVCFLLAKNK YFQKFVTAVL VITSVLLALE DIYLPQRPVL VNITLYVDYV LTAFFVIEMI IMLFAVGFKK Y FTSKWYWL DFIVVVAYLL NFVLMCAGIE ALQTLRLLRV FRLFRPLSKV NGMQVVTSTL VEAVPHIFNV ILVGIFFWLV FA IMGVQLF AGKFYKCVDE NSTVLSHEIT MDRNDCLHEN YTWENSPMNF DHVGNAYLSL LQVATFKGWL QIMNDAIDSR EVH KQPIRE TNIYMYLYFI FFIVFGSFFI LKLFVCILID IFRQQRRKAE GLSATDSRTQ LIYRRAVMRT MSAKPVKRIP KPTC HPQSL MYDISVNRKF EYTMMILIIL NVAVMAIDHY GQSMEFSEVL DYLNLIFIII FFVECVIKVS GLRHHYFKDP WNIID FLYV VLAIAGLMLS DVIEKYFISP TLLRILRILR VGRLLRYFQS ARGMRLLLLA LRKALRTLFN VSFLLFVIMF VYAVFG MEF FMHIRDAGAI DDVYNFKTFG QSIILLFQLA TSAGWDGVYF AIANEEDCRA PDHELGYPGN CGSRALGIAY LVSYLII TC LVVINMYAAV ILDYVLEVYE DSKEGLTDDD YDMFFEVWQQ FDPEATQYIR YDQLSELLEA LQPPLQVQKP NKYKILSM N IPICKDDHIF YKDVLEALVK DVFSRRGSPV EAGDVQAPNV DEAEYKPVSS TLQRQREEYC VRLIQNAWRK HKQQN

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Macromolecule #2: N-ACETYL-D-GLUCOSAMINE

MacromoleculeName: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 2 / Number of copies: 13 / Formula: NAG
Molecular weightTheoretical: 221.208 Da

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Macromolecule #3: BETA-D-MANNOSE

MacromoleculeName: BETA-D-MANNOSE / type: ligand / ID: 3 / Number of copies: 7 / Formula: BMA
Molecular weightTheoretical: 180.156 Da

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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 mg/mL
BufferpH: 7.4
Details: 25 mM Tris-HCl, pH 7.4, 50mM NaCl, 0.1% digitonin, 2.5 mM D-Desthiobiotin and protease inhibitor cocktail
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K
Details: Grids were blotted for 3.5 s and flash-frozen in liquid ethane cooled by liquid nitrogen..
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.6 µm / Calibrated defocus min: 1.7 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 22500
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average exposure time: 0.25 sec. / Average electron dose: 1.5625 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4739175
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

9513

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 1373581

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