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- EMDB-9617: Structure of the human voltage-gated sodium channel Nav1.4 in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-9617
TitleStructure of the human voltage-gated sodium channel Nav1.4 in complex with beta1
Map data
Sample
  • Complex: Complex of human sodium channel protein type 4 subunit alpha and human sodium channel subunit beta-1
    • Complex: Human sodium channel protein type 4 subunit alpha
      • Protein or peptide: Sodium channel protein type 4 subunit alpha
    • Complex: Human sodium channel subunit beta-1
      • Protein or peptide: Sodium channel subunit beta-1
  • Ligand: N-ACETYL-D-GLUCOSAMINE
  • Ligand: BETA-D-MANNOSE
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
Function / homology
Function and homology information


regulation of skeletal muscle contraction by action potential / corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / regulation of sodium ion transmembrane transport / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport ...regulation of skeletal muscle contraction by action potential / corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / regulation of sodium ion transmembrane transport / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / node of Ranvier / sodium channel inhibitor activity / membrane depolarization during action potential / voltage-gated sodium channel complex / cardiac muscle cell action potential involved in contraction / locomotion / regulation of ventricular cardiac muscle cell membrane repolarization / neuronal action potential propagation / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / membrane depolarization / intercalated disc / sodium channel regulator activity / sodium ion transmembrane transport / cardiac muscle contraction / muscle contraction / T-tubule / axon guidance / positive regulation of neuron projection development / Sensory perception of sweet, bitter, and umami (glutamate) taste / perikaryon / transmembrane transporter binding / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Voltage gated sodium channel, alpha-4 subunit, mammalian / Sodium channel subunit beta-1/beta-3 / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / IQ motif profile. / Voltage-dependent channel domain superfamily / Immunoglobulin V-set domain ...Voltage gated sodium channel, alpha-4 subunit, mammalian / Sodium channel subunit beta-1/beta-3 / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / IQ motif profile. / Voltage-dependent channel domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ion transport domain / Ion transport protein / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sodium channel protein type 4 subunit alpha / Sodium channel regulatory subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPan XJ / li ZQ / Zhou Q / Shen HZ / Wu K / Huang XS / Chen JF / Zhang JR / Zhu XC / Lei JL ...Pan XJ / li ZQ / Zhou Q / Shen HZ / Wu K / Huang XS / Chen JF / Zhang JR / Zhu XC / Lei JL / Xiong W / Gong HP / Xiao BL / Yan N
CitationJournal: Science / Year: 2018
Title: Structure of the human voltage-gated sodium channel Na1.4 in complex with β1.
Authors: Xiaojing Pan / Zhangqiang Li / Qiang Zhou / Huaizong Shen / Kun Wu / Xiaoshuang Huang / Jiaofeng Chen / Juanrong Zhang / Xuechen Zhu / Jianlin Lei / Wei Xiong / Haipeng Gong / Bailong Xiao / Nieng Yan /
Abstract: Voltage-gated sodium (Na) channels, which are responsible for action potential generation, are implicated in many human diseases. Despite decades of rigorous characterization, the lack of a structure ...Voltage-gated sodium (Na) channels, which are responsible for action potential generation, are implicated in many human diseases. Despite decades of rigorous characterization, the lack of a structure of any human Na channel has hampered mechanistic understanding. Here, we report the cryo-electron microscopy structure of the human Na1.4-β1 complex at 3.2-Å resolution. Accurate model building was made for the pore domain, the voltage-sensing domains, and the β1 subunit, providing insight into the molecular basis for Na permeation and kinetic asymmetry of the four repeats. Structural analysis of reported functional residues and disease mutations corroborates an allosteric blocking mechanism for fast inactivation of Na channels. The structure provides a path toward mechanistic investigation of Na channels and drug discovery for Na channelopathies.
History
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
DepositionAug 11, 2018-
UpdateDec 26, 2018-
Current statusDec 26, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6agf
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9617.png

Downloads & links

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Map

FileDownload / File: emd_9617.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 261.84 Å		1.09 Å/pix.
x 240 pix.
= 261.84 Å		1.09 Å/pix.
x 240 pix.
= 261.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.18689415 - 0.32327962
Average (Standard dev.)0.0007376144 (±0.0091986805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 261.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z261.840261.840261.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1870.3230.001

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Supplemental data

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Sample components

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Entire : Complex of human sodium channel protein type 4 subunit alpha and ...

EntireName: Complex of human sodium channel protein type 4 subunit alpha and human sodium channel subunit beta-1
Components
  • Complex: Complex of human sodium channel protein type 4 subunit alpha and human sodium channel subunit beta-1
    • Complex: Human sodium channel protein type 4 subunit alpha
      • Protein or peptide: Sodium channel protein type 4 subunit alpha
    • Complex: Human sodium channel subunit beta-1
      • Protein or peptide: Sodium channel subunit beta-1
  • Ligand: N-ACETYL-D-GLUCOSAMINE
  • Ligand: BETA-D-MANNOSE
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en

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Supramolecule #1: Complex of human sodium channel protein type 4 subunit alpha and ...

SupramoleculeName: Complex of human sodium channel protein type 4 subunit alpha and human sodium channel subunit beta-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: Human sodium channel protein type 4 subunit alpha

SupramoleculeName: Human sodium channel protein type 4 subunit alpha / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Human sodium channel subunit beta-1

SupramoleculeName: Human sodium channel subunit beta-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Sodium channel protein type 4 subunit alpha

MacromoleculeName: Sodium channel protein type 4 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 212.836375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMARPSLC TLVPLGPECL RPFTRESLAA IEQRAVEEEA RLQRNKQME IEEPERKPRS DLEAGKNLPM IYGDPPPEVI GIPLEDLDPY YSNKKTFIVL NKGKAIFRFS ATPALYLLSP F SVVRRGAI ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMARPSLC TLVPLGPECL RPFTRESLAA IEQRAVEEEA RLQRNKQME IEEPERKPRS DLEAGKNLPM IYGDPPPEVI GIPLEDLDPY YSNKKTFIVL NKGKAIFRFS ATPALYLLSP F SVVRRGAI KVLIHALFSM FIMITILTNC VFMTMSDPPP WSKNVEYTFT GIYTFESLIK ILARGFCVDD FTFLRDPWNW LD FSVIMMA YLTEFVDLGN ISALRTFRVL RALKTITVIP GLKTIVGALI QSVKKLSDVM ILTVFCLSVF ALVGLQLFMG NLR QKCVRW PPPFNDTNTT WYSNDTWYGN DTWYGNEMWY GNDSWYANDT WNSHASWATN DTFDWDAYIS DEGNFYFLEG SNDA LLCGN SSDAGHCPEG YECIKTGRNP NYGYTSYDTF SWAFLALFRL MTQDYWENLF QLTLRAAGKT YMIFFVVIIF LGSFY LINL ILAVVAMAYA EQNEATLAED KEKEEEFQQM LEKFKKHQEE LEKAKAAQAL EGGEADGDPA HGKDCNGSLD TSQGEK GAP RQSSSGDSGI SDAMEELEEA HQKCPPWWYK CAHKVLIWNC CAPWLKFKNI IHLIVMDPFV DLGITICIVL NTLFMAM EH YPMTEHFDNV LTVGNLVFTG IFTAEMVLKL IAMDPYEYFQ QGWNIFDSII VTLSLVELGL ANVQGLSVLR SFRLLRVF K LAKSWPTLNM LIKIIGNSVG ALGNLTLVLA IIVFIFAVVG MQLFGKSYKE CVCKIALDCN LPRWHMHDFF HSFLIVFRI LCGEWIETMW DCMEVAGQAM CLTVFLMVMV IGNLVVLNLF LALLLSSFSA DSLAASDEDG EMNNLQIAIG RIKLGIGFAK AFLLGLLHG KILSPKDIML SLGEADGAGE AGEAGETAPE DEKKEPPEED LKKDNHILNH MGLADGPPSS LELDHLNFIN N PYLTIQVP IASEESDLEM PTEEETDTFS EPEDSKKPPQ PLYDGNSSVC STADYKPPEE DPEEQAEENP EGEQPEECFT EA CVQRWPC LYVDISQGRG KKWWTLRRAC FKIVEHNWFE TFIVFMILLS SGALAFEDIY IEQRRVIRTI LEYADKVFTY IFI MEMLLK WVAYGFKVYF TNAWCWLDFL IVDVSIISLV ANWLGYSELG PIKSLRTLRA LRPLRALSRF EGMRVVVNAL LGAI PSIMN VLLVCLIFWL IFSIMGVNLF AGKFYYCINT TTSERFDISE VNNKSECESL MHTGQVRWLN VKVNYDNVGL GYLSL LQVA TFKGWMDIMY AAVDSREKEE QPQYEVNLYM YLYFVIFIIF GSFFTLNLFI GVIIDNFNQQ KKKLGGKDIF MTEEQK KYY NAMKKLGSKK PQKPIPRPQN KIQGMVYDLV TKQAFDITIM ILICLNMVTM MVETDNQSQL KVDILYNINM IFIIIFT GE CVLKMLALRQ YYFTVGWNIF DFVVVILSIV GLALSDLIQK YFVSPTLFRV IRLARIGRVL RLIRGAKGIR TLLFALMM S LPALFNIGLL LFLVMFIYSI FGMSNFAYVK KESGIDDMFN FETFGNSIIC LFEITTSAGW DGLLNPILNS GPPDCDPNL ENPGTSVKGD CGNPSIGICF FCSYIIISFL IVVNMYIAII LENFNVATEE SSEPLGEDDF EMFYETWEKF DPDATQFIAY SRLSDFVDT LQEPLRIAKP NKIKLITLDL PMVPGDKIHC LDILFALTKE VLGDSGEMDA LKQTMEEKFM AANPSKVSYE P ITTTLKRK HEEVCAIKIQ RAYRRHLLQR SMKQASYMYR HSHDGSGDDA PEKEGLLANT MSKMYGHENG NSSSPSPEEK GE AGDAGPT MGLMPISPSD TAWPPAPPPG QTVRPGVKES LV

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Macromolecule #2: Sodium channel subunit beta-1

MacromoleculeName: Sodium channel subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.732115 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRLLALVVG AALVSSACGG CVEVDSETEA VYGMTFKILC ISCKRRSETN AETFTEWTFR QKGTEEFVKI LRYENEVLQL EEDERFEGR VVWNGSRGTK DLQDLSIFIT NVTYNHSGDY ECHVYRLLFF ENYEHNTSVV KKIHIEVVDK ANRDMASIVS E IMMYVLIV ...String:
MGRLLALVVG AALVSSACGG CVEVDSETEA VYGMTFKILC ISCKRRSETN AETFTEWTFR QKGTEEFVKI LRYENEVLQL EEDERFEGR VVWNGSRGTK DLQDLSIFIT NVTYNHSGDY ECHVYRLLFF ENYEHNTSVV KKIHIEVVDK ANRDMASIVS E IMMYVLIV VLTIWLVAEM IYCYKKIAAA TETAAQENAS EYLAITSESK ENCTGVQVAE

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Macromolecule #3: N-ACETYL-D-GLUCOSAMINE

MacromoleculeName: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da

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Macromolecule #4: BETA-D-MANNOSE

MacromoleculeName: BETA-D-MANNOSE / type: ligand / ID: 4 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da

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Macromolecule #5: [(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: 5 / Number of copies: 6 / 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

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Macromolecule #6: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 6 / Number of copies: 1 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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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

BufferpH: 5.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 48.0 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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 191936
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)

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