[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleUnwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na1.7.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 33, Page e2209164119, Year 2022
Publish dateAug 16, 2022
AuthorsGaoxingyu Huang / Qiurong Wu / Zhangqiang Li / Xueqin Jin / Xiaoshuang Huang / Tong Wu / Xiaojing Pan / Nieng Yan /
PubMed AbstractVoltage-gated sodium (Na) channel Na1.7 has been targeted for the development of nonaddictive pain killers. Structures of Na1.7 in distinct functional states will offer an advanced mechanistic ...Voltage-gated sodium (Na) channel Na1.7 has been targeted for the development of nonaddictive pain killers. Structures of Na1.7 in distinct functional states will offer an advanced mechanistic understanding and aid drug discovery. Here we report the cryoelectron microscopy analysis of a human Na1.7 variant that, with 11 rationally introduced point mutations, has a markedly right-shifted activation voltage curve with V reaching 69 mV. The voltage-sensing domain in the first repeat (VSD) in a 2.7-Å resolution structure displays a completely down (deactivated) conformation. Compared to the structure of WT Na1.7, three gating charge (GC) residues in VSD are transferred to the cytosolic side through a combination of helix unwinding and spiral sliding of S4 and ∼20° domain rotation. A conserved WNФФD motif on the cytoplasmic end of S3 stabilizes the down conformation of VSD. One GC residue is transferred in VSD mainly through helix sliding. Accompanying GC transfer in VSD and VSD, rearrangement and contraction of the intracellular gate is achieved through concerted movements of adjacent segments, including S4-5, S4-5, S5, and all S6 segments. Our studies provide important insight into the electromechanical coupling mechanism of the single-chain voltage-gated ion channels and afford molecular interpretations for a number of pain-associated mutations whose pathogenic mechanism cannot be revealed from previously reported Na structures.
External linksProc Natl Acad Sci U S A / PubMed:35878056 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 2.8 Å
Structure data

33484

7xve

EMDB-33484, PDB-7xve:
Human Nav1.7 mutant class-I
Method: EM (single particle) / Resolution: 2.7 Å

33485

7xvf

EMDB-33485, PDB-7xvf:
Nav1.7 mutant class2
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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

ChemComp-1PW:
(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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

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

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / Membrane protein. / MEMBRANE PROTEIN / action potential

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more