[English] 日本語
Yorodumi
- PDB-6sxe: Crystal Structure of the Voltage-Gated Sodium Channel NavMs (F208... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sxe
TitleCrystal Structure of the Voltage-Gated Sodium Channel NavMs (F208L) in complex with Endoxifen (2.6 Angstrom resolution)
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein
Function / homology
Function and homology information


voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / Endoxifen / Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSula, A. / Hollingworth, D. / Wallace, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006790, BB/N012763 and BB/R001294 United Kingdom
CitationJournal: Mol.Cell / Year: 2021
Title: A tamoxifen receptor within a voltage-gated sodium channel.
Authors: Sula, A. / Hollingworth, D. / Ng, L.C.T. / Larmore, M. / DeCaen, P.G. / Wallace, B.A.
History
DepositionSep 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1459
Polymers31,1861
Non-polymers1,9598
Water90150
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,58036
Polymers124,7434
Non-polymers7,83832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area23120 Å2
ΔGint-215 kcal/mol
Surface area51710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.108, 110.108, 210.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-302-

NA

31A-303-

NA

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ion transport protein


Mass: 31185.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L5S6

-
Non-polymers , 5 types, 58 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#5: Chemical ChemComp-9XY / Endoxifen / 4-[(1Z)-1-{4-[2-(methylamino)ethoxy]phenyl}-2-phenylbut-1-en-1-yl]phenol


Mass: 373.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M MgCl2 hexahydrate, 0.1 M HEPES buffer, pH 8, 30% v/v polyethylene glycol (PEG) 500 and 4% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97966 Å / Relative weight: 1
ReflectionResolution: 2.6→52.54 Å / Num. obs: 20152 / % possible obs: 99.1 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2435 / CC1/2: 0.826 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVX

5hvx


Resolution: 2.6→52.54 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.87 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.278 939 4.66 %RANDOM
Rwork0.238 ---
obs0.24 20151 99.1 %-
Displacement parametersBiso max: 276.3 Å2 / Biso mean: 108.44 Å2 / Biso min: 45.82 Å2
Baniso -1Baniso -2Baniso -3
1--12.5915 Å20 Å20 Å2
2---12.5915 Å20 Å2
3---25.183 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.6→52.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 114 50 2309
Biso mean--142.45 95.03 -
Num. residues----271
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d829SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes416HARMONIC5
X-RAY DIFFRACTIONt_it2305HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion301SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2721SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2305HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3107HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion20.23
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 46
RfactorNum. reflection% reflection
Rfree0.1975 20 4.56 %
Rwork0.2112 419 -
all0.2104 439 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.2493 Å / Origin y: 6.0926 Å / Origin z: 32.0674 Å
111213212223313233
T-0.3479 Å2-0.0771 Å2-0.1087 Å2--0.2518 Å2-0.009 Å2---0.4198 Å2
L0.5145 °2-0.0893 °20.3224 °2-1.219 °20.2929 °2--2.3405 °2
S-0.0833 Å °-0.1643 Å °0.074 Å °0.2883 Å °0.0202 Å °-0.2849 Å °-0.2841 Å °0.6257 Å °0.0631 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlvh1.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