[English] 日本語
Yorodumi
- PDB-6n4r: CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6n4r
TitleCryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2
Components
  • Beta/omega-theraphotoxin-Tp2a
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Nav1.7 VSD2-NavAb chimera
KeywordsMEMBRANE PROTEIN / voltage-gated sodium channel / gating modifier toxin
Function / homologyCytoplasmic domain of voltage-gated Na+ ion channel / Interaction between L1 and Ankyrins / Sodium ion transport-associated / Ion transport protein / Voltage gated sodium channel, alpha-9 subunit / Phase 0 - rapid depolarisation / Voltage-dependent channel domain superfamily / Voltage-gated Na+ ion channel, cytoplasmic domain / Sodium ion transport-associated / Ion transport domain ...Cytoplasmic domain of voltage-gated Na+ ion channel / Interaction between L1 and Ankyrins / Sodium ion transport-associated / Ion transport protein / Voltage gated sodium channel, alpha-9 subunit / Phase 0 - rapid depolarisation / Voltage-dependent channel domain superfamily / Voltage-gated Na+ ion channel, cytoplasmic domain / Sodium ion transport-associated / Ion transport domain / Voltage gated sodium channel, alpha subunit / IQ motif, EF-hand binding site / voltage-gated sodium channel complex / membrane depolarization during action potential / behavioral response to pain / voltage-gated sodium channel activity / sodium ion binding / neuronal action potential / sodium ion transmembrane transport / voltage-gated ion channel activity / sodium ion transport / regulation of ion transmembrane transport / sensory perception of pain / post-embryonic development / response to toxic substance / ion channel activity / toxin activity / lipid binding / inflammatory response / axon / integral component of plasma membrane / integral component of membrane / extracellular region / identical protein binding / plasma membrane / Ion transport protein / Beta/omega-theraphotoxin-Tp2a / Sodium channel protein type 9 subunit alpha
Function and homology information
Specimen sourceArcobacter butzleri (bacteria)
Homo sapiens (human)
Mus musculus (house mouse)
Thrixopelma pruriens (green velvet)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsXu, H. / Rohou, A. / Arthur, C.P. / Estevez, A. / Ciferri, C. / Payandeh, J. / Koth, C.M.
CitationJournal: Cell / Year: 2019
Title: Structural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin.
Authors: Hui Xu / Tianbo Li / Alexis Rohou / Christopher P Arthur / Foteini Tzakoniati / Evera Wong / Alberto Estevez / Christine Kugel / Yvonne Franke / Jun Chen / Claudio Ciferri / David H Hackos / Christopher M Koth / Jian Payandeh
Abstract: Voltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and ...Voltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and toxin modulation remains ill-defined. Protoxin-II (ProTx2) from the Peruvian green velvet tarantula is an inhibitor cystine-knot peptide and selective antagonist of the human Nav1.7 channel. Here, we visualize ProTx2 in complex with voltage-sensor domain II (VSD2) from Nav1.7 using X-ray crystallography and cryoelectron microscopy. Membrane partitioning orients ProTx2 for unfettered access to VSD2, where ProTx2 interrogates distinct features of the Nav1.7 receptor site. ProTx2 positions two basic residues into the extracellular vestibule to antagonize S4 gating-charge movement through an electrostatic mechanism. ProTx2 has trapped activated and deactivated states of VSD2, revealing a remarkable ∼10 Å translation of the S4 helix, providing a structural framework for activation gating in voltage-gated ion channels. Finally, our results deliver key templates to design selective Nav channel antagonists.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2018 / Release: Jan 23, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 23, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0342
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Nav1.7 VSD2-NavAb chimera
C: Nav1.7 VSD2-NavAb chimera
D: Nav1.7 VSD2-NavAb chimera
E: Beta/omega-theraphotoxin-Tp2a
F: Beta/omega-theraphotoxin-Tp2a
G: Beta/omega-theraphotoxin-Tp2a
H: Beta/omega-theraphotoxin-Tp2a
I: Fab light chain
J: Fab heavy chain
K: Fab light chain
L: Fab heavy chain
A: Nav1.7 VSD2-NavAb chimera


Theoretical massNumber of molelcules
Total (without water)245,18812
Polyers245,18812
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide
Nav1.7 VSD2-NavAb chimera / Neuroendocrine sodium channel / hNE-Na / Peripheral sodium channel 1 / PN1 / Sodium channel protein type IX subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.7


Mass: 33453.512 Da / Num. of mol.: 4
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: RM4018 / Gene: Abu_1752, SCN9A, NENA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5, UniProt: Q15858
#2: Protein/peptide
Beta/omega-theraphotoxin-Tp2a / Beta/omega-TRTX-Tp2a / ProTx-II / PT-II / Protoxin-2 / ProTx2


Mass: 3839.687 Da / Num. of mol.: 4 / Source: (synth.) Thrixopelma pruriens (green velvet) / References: UniProt: P83476
#3: Protein/peptide Fab light chain / Fragment antigen-binding


Mass: 23483.910 Da / Num. of mol.: 2 / Source: (natural) Mus musculus (house mouse)
#4: Protein/peptide Fab heavy chain / Fragment antigen-binding


Mass: 24523.518 Da / Num. of mol.: 2 / Source: (natural) Mus musculus (house mouse)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Nav1.7 VSD2 in complex with ProTx2 and an anti-Nav Fab
Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.245 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionDetails: 10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1
pH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grid was coated with a thin layer of gold / Grid material: COPPER / Grid mesh size: 300 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 41 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 25084
Image scansMovie frames/image: 40

-
Processing

EM software
IDNameVersionCategory
1cisTEM1.0.0particle selection
2SerialEMimage acquisition
4cisTEM1.0.0CTF correction
10cisTEM1.0.0initial Euler assignment
11cisTEM1.0.0final Euler assignment
12cisTEM1.0.0classification
13cisTEM1.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53206
Details: Spatial frequencies higher than 8 Angstroms were not used during refinement.
Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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