[English] 日本語
Yorodumi
- PDB-4l1d: Voltage-gated sodium channel beta3 subunit Ig domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l1d
TitleVoltage-gated sodium channel beta3 subunit Ig domain
ComponentsSodium channel subunit beta-3
KeywordsMEMBRANE PROTEIN / V-type immunoglobulin fold / sodium channel / voltage-gated / sodium channel alpha subunit / membrane
Function / homology
Function and homology information


SA node cell action potential / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport ...SA node cell action potential / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cardiac muscle cell action potential involved in contraction / ventricular cardiac muscle cell action potential / sodium channel inhibitor activity / Interaction between L1 and Ankyrins / positive regulation of heart rate / sodium ion transport / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / membrane depolarization / sodium ion transmembrane transport / sodium channel regulator activity / cardiac muscle contraction / protein localization to plasma membrane / Z disc / nervous system development / transmembrane transporter binding / membrane / plasma membrane
Similarity search - Function
Sodium channel subunit beta-1/beta-3 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Sodium channel subunit beta-1/beta-3 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium channel regulatory subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNamadurai, S. / Weimhofer, M. / Rajappa, R. / Stott, K. / Klingauf, J. / Chirgadze, D.Y. / Jackson, A.P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure and Molecular Imaging of the Nav Channel beta 3 Subunit Indicates a Trimeric Assembly.
Authors: Namadurai, S. / Balasuriya, D. / Rajappa, R. / Wiemhofer, M. / Stott, K. / Klingauf, J. / Edwardson, J.M. / Chirgadze, D.Y. / Jackson, A.P.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sodium channel subunit beta-3
B: Sodium channel subunit beta-3
C: Sodium channel subunit beta-3


Theoretical massNumber of molelcules
Total (without water)44,4983
Polymers44,4983
Non-polymers00
Water2,108117
1
A: Sodium channel subunit beta-3


Theoretical massNumber of molelcules
Total (without water)14,8331
Polymers14,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sodium channel subunit beta-3


Theoretical massNumber of molelcules
Total (without water)14,8331
Polymers14,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sodium channel subunit beta-3


Theoretical massNumber of molelcules
Total (without water)14,8331
Polymers14,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.469, 81.469, 114.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0

-
Components

#1: Protein Sodium channel subunit beta-3 /


Mass: 14832.702 Da / Num. of mol.: 3 / Fragment: Ig domain, UNP residues 25-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1158, SCN3B / Plasmid: pTT3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9NY72
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1M Sodium citrate tribasic, 0.1M CHES/Sodium hydroxide pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 15706 / Num. obs: 15675 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2257 / Rsym value: 0.633 / % possible all: 100

-
Processing

Software
NameVersionClassification
GDAdata collection
PHENIX(phenix.phaser: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X1X, 1I8L AND 1F97

2x1x

1i8l

1f97


Resolution: 2.5→30 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1560 9.97 %Random
Rwork0.2017 ---
all0.2053 15674 --
obs0.2053 15643 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 0 117 2753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082693
X-RAY DIFFRACTIONf_angle_d1.2453643
X-RAY DIFFRACTIONf_dihedral_angle_d16.822977
X-RAY DIFFRACTIONf_chiral_restr0.072412
X-RAY DIFFRACTIONf_plane_restr0.004469
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1504X-RAY DIFFRACTION12.423TORSIONAL
12B1504X-RAY DIFFRACTION12.423TORSIONAL
13C1504X-RAY DIFFRACTION12.423TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58070.31141390.27191252X-RAY DIFFRACTION100
2.5807-2.67290.3061420.24631273X-RAY DIFFRACTION100
2.6729-2.77980.29731400.25481238X-RAY DIFFRACTION100
2.7798-2.90620.2591450.23951280X-RAY DIFFRACTION100
2.9062-3.05930.2981340.23531266X-RAY DIFFRACTION100
3.0593-3.25080.26071420.20831281X-RAY DIFFRACTION100
3.2508-3.50140.25891400.19921261X-RAY DIFFRACTION100
3.5014-3.85310.21981380.18061276X-RAY DIFFRACTION100
3.8531-4.40920.2041450.16911289X-RAY DIFFRACTION100
4.4092-5.54940.19791420.16371300X-RAY DIFFRACTION99
5.5494-30.01780.23321530.22611367X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7064-0.21050.26182.93751.73913.28280.0706-0.1052-0.0890.13140.12-0.30030.1098-0.06340.24560.05250.0139-0.06820.0274-0.00940.021355.54724.065125.4074
23.102-0.4183-0.49953.22661.08483.19540.40280.02170.381-1.0018-0.5060.0468-1.0006-0.723-0.25010.39540.21930.05430.25170.02780.204333.707239.2507126.3412
33.8531.25171.70414.6828-1.11342.6342-0.08010.0124-0.3424-0.25350.41671.00410.3819-0.29620.11770.1090.04840.00790.2060.05150.401831.402213.0991124.6894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'

+
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