[English] 日本語
Yorodumi
- EMDB-32451: Human Nav1.8 with A-803467, class II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32451
TitleHuman Nav1.8 with A-803467, class II
Map data
Sample
  • Complex: sodium channel II
    • Protein or peptide: Sodium channel protein type 10 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
KeywordsVoltage-gated sodium channel / Nav / activation / selectivity / MEMBRANE PROTEIN
Function / homology
Function and homology information


bundle of His cell action potential / AV node cell action potential / clathrin complex / regulation of atrial cardiac muscle cell membrane depolarization / sensory perception / membrane depolarization during action potential / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / voltage-gated sodium channel complex / cardiac muscle cell action potential involved in contraction / regulation of monoatomic ion transmembrane transport ...bundle of His cell action potential / AV node cell action potential / clathrin complex / regulation of atrial cardiac muscle cell membrane depolarization / sensory perception / membrane depolarization during action potential / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / voltage-gated sodium channel complex / cardiac muscle cell action potential involved in contraction / regulation of monoatomic ion transmembrane transport / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / Phase 0 - rapid depolarisation / odontogenesis of dentin-containing tooth / regulation of cardiac muscle contraction / sodium ion transmembrane transport / regulation of heart rate / presynaptic membrane / transmembrane transporter binding / axon / glutamatergic synapse / extracellular exosome / plasma membrane
Similarity search - Function
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 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein type 10 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYan N / Pan XJ
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural basis for high-voltage activation and subtype-specific inhibition of human Na1.8.
Authors: Xiaoshuang Huang / Xueqin Jin / Gaoxingyu Huang / Jian Huang / Tong Wu / Zhangqiang Li / Jiaofeng Chen / Fang Kong / Xiaojing Pan / Nieng Yan /
Abstract: The dorsal root ganglia-localized voltage-gated sodium (Na) channel Na1.8 represents a promising target for developing next-generation analgesics. A prominent characteristic of Na1.8 is the ...The dorsal root ganglia-localized voltage-gated sodium (Na) channel Na1.8 represents a promising target for developing next-generation analgesics. A prominent characteristic of Na1.8 is the requirement of more depolarized membrane potential for activation. Here we present the cryogenic electron microscopy structures of human Na1.8 alone and bound to a selective pore blocker, A-803467, at overall resolutions of 2.7 to 3.2 Å. The first voltage-sensing domain (VSD) displays three different conformations. Structure-guided mutagenesis identified the extracellular interface between VSD and the pore domain (PD) to be a determinant for the high-voltage dependence of activation. A-803467 was clearly resolved in the central cavity of the PD, clenching S6. Our structure-guided functional characterizations show that two nonligand binding residues, Thr397 on S6 and Gly1406 on S6, allosterically modulate the channel's sensitivity to A-803467. Comparison of available structures of human Na channels suggests the extracellular loop region to be a potential site for developing subtype-specific pore-blocking biologics.
History
DepositionDec 23, 2021-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32451.png

Downloads & links

-
Map

FileDownload / File: emd_32451.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.)
1.08 Å/pix.
x 240 pix.
= 259.8 Å		1.08 Å/pix.
x 240 pix.
= 259.8 Å		1.08 Å/pix.
x 240 pix.
= 259.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0171
Minimum - Maximum-0.045831837 - 0.11893008
Average (Standard dev.)0.00047232845 (±0.0028954477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : sodium channel II

EntireName: sodium channel II
Components
  • Complex: sodium channel II
    • Protein or peptide: Sodium channel protein type 10 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

-
Supramolecule #1: sodium channel II

SupramoleculeName: sodium channel II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Sodium channel protein type 10 subunit alpha

MacromoleculeName: Sodium channel protein type 10 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220.9035 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC NQLPKFYGEL PAELIGEPLE DLDPFYSTH RTFMVLNKGR TISRFSATRA LWLFSPFNLI RRTAIKVSVH SWFSLFITVT ILVNCVCMTR TDLPEKIEYV F TVIYTFEA ...String:
MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC NQLPKFYGEL PAELIGEPLE DLDPFYSTH RTFMVLNKGR TISRFSATRA LWLFSPFNLI RRTAIKVSVH SWFSLFITVT ILVNCVCMTR TDLPEKIEYV F TVIYTFEA LIKILARGFC LNEFTYLRDP WNWLDFSVIT LAYVGTAIDL RGISGLRTFR VLRALKTVSV IPGLKVIVGA LI HSVKKLA DVTILTIFCL SVFALVGLQL FKGNLKNKCV KNDMAVNETT NYSSHRKPDI YINKRGTSDP LLCGNGSDSG HCP DGYICL KTSDNPDFNY TSFDSFAWAF LSLFRLMTQD SWERLYQQTL RTSGKIYMIF FVLVIFLGSF YLVNLILAVV TMAY EEQNQ ATTDEIEAKE KKFQEALEML RKEQEVLAAL GIDTTSLHSH NGSPLTSKNA SERRHRIKPR VSEGSTEDNK SPRSD PYNQ RRMSFLGLAS GKRRASHGSV FHFRSPGRDI SLPEGVTDDG VFPGDHESHR GSLLLGGGAG QQGPLPRSPL PQPSNP DSR HGEDEHQPPP TSELAPGAVD VSAFDAGQKK TFLSAEYLDE PFRAQRAMSV VSIITSVLEE LEESEQKCPP CLTSLSQ KY LIWDCCPMWV KLKTILFGLV TDPFAELTIT LCIVVNTIFM AMEHHGMSPT FEAMLQIGNI VFTIFFTAEM VFKIIAFD P YYYFQKKWNI FDCIIVTVSL LELGVAKKGS LSVLRSFRLL RVFKLAKSWP TLNTLIKIIG NSVGALGNLT IILAIIVFV FALVGKQLLG ENYRNNRKNI SAPHEDWPRW HMHDFFHSFL IVFRILCGEW IENMWACMEV GQKSICLILF LTVMVLGNLV VLNLFIALL LNSFFADNLT APEDDGEVNN LQVALARIQV FGHRTKQALC SFFSRSCPFP QPKAEPELVV KLPLSSSKAE N HIAANTAR GSSGGLQAPR GPRDEHSDFI ANPTVWVSVP IAEGESDLDD LEDDGGEDAQ SFQQEVIPKG QQEQLQQVER CG DHLTPRS PGTGTSSEDL APSLGETWKD ESVPQVPAEG VDDTSSSEGS TVDCLDPEEI LRKIPELADD LEEPDDCFTE GCI RHCPCC KLDTTKSPWD VGWQVRKTCY RIVEHSWFES FIIFMILLSS GSLAFEDYYL DQKPTVKALL EYTDRVFTFI FVFE MLLKW VAYGFKKYFT NAWCWLDFLI VNISLISLTA KILEYSEVAP IKALRTLRAL RPLRALSRFE GMRVVVDALV GAIPS IMNV LLVCLIFWLI FSIMGVNLFA GKFWRCINYT DGEFSLVPLS IVNNKSDCKI QNSTGSFFWV NVKVNFDNVA MGYLAL LQV ATFKGWMDIM YAAVDSREVN MQPKWEDNVY MYLYFVIFII FGGFFTLNLF VGVIIDNFNQ QKKKLGGQDI FMTEEQK KY YNAMKKLGSK KPQKPIPRPL NKFQGFVFDI VTRQAFDITI MVLICLNMIT MMVETDDQSE EKTKILGKIN QFFVAVFT G ECVMKMFALR QYYFTNGWNV FDFIVVVLSI ASLIFSAILK SLQSYFSPTL FRVIRLARIG RILRLIRAAK GIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMSSFP HVRWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP NLPNSNGTR GDCGSPAVGI IFFTTYIIIS FLIMVNMYIA VILENFNVAT EESTEPLSED DFDMFYETWE KFDPEATQFI T FSALSDFA DTLSGPLRIP KPNRNILIQM DLPLVPGDKI HCLDILFAFT KNVLGESGEL DSLKANMEEK FMATNLSKSS YE PIATTLR WKQEDISATV IQKAYRSYVL HRSMALSNTP CVPRAEEEAA SLPDEGFVAF TANENCVLPD KSETASATSF PPS YESVTR GLSDRVNMRT SSSIQNEDEA TSMELIAPGP

UniProtKB: Sodium channel protein type 10 subunit alpha

-
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: 5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide

MacromoleculeName: 5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: 95T
Molecular weightTheoretical: 357.788 Da
Chemical component information

ChemComp-95T:
5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide

-
Macromolecule #5: CHOLESTEROL

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

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #6: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 7 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

-
Macromolecule #7: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 7 / Number of copies: 12 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

ChemComp-LPE:
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

-
Macromolecule #8: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 8 / Number of copies: 2 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

-
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 K3 (6k 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141848
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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://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