[English] 日本語
Yorodumi
- PDB-4jq0: Voltage-gated sodium channel 1.5 C-terminal domain in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jq0
TitleVoltage-gated sodium channel 1.5 C-terminal domain in complex with FGF12B and Ca2+/calmodulin
Components
  • Calmodulin
  • Fibroblast growth factor 12
  • Sodium channel protein type 5 subunit alpha
KeywordsTRANSPORT PROTEIN / EF hand / ion channel / membrane
Function / homology
Function and homology information


regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / regulation of ventricular cardiac muscle cell membrane depolarization / regulation of neuronal action potential / AV node cell action potential / SA node cell action potential ...regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / regulation of ventricular cardiac muscle cell membrane depolarization / regulation of neuronal action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation / membrane depolarization during atrial cardiac muscle cell action potential / cardiac ventricle development / regulation of atrial cardiac muscle cell membrane repolarization / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / brainstem development / membrane depolarization during AV node cell action potential / membrane depolarization during bundle of His cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / positive regulation of action potential / membrane depolarization during Purkinje myocyte cell action potential / atrial cardiac muscle cell action potential / telencephalon development / : / : / : / : / cardiac conduction system development / : / positive regulation of protein autophosphorylation / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport / regulation of sodium ion transmembrane transport / negative regulation of peptidyl-threonine phosphorylation / ventricular cardiac muscle cell action potential / establishment of protein localization to mitochondrial membrane / regulation of ventricular cardiac muscle cell membrane repolarization / type 3 metabotropic glutamate receptor binding / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / regulation of cardiac muscle cell contraction / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / Interaction between L1 and Ankyrins / Sodium/Calcium exchangers / ankyrin binding / Calmodulin induced events / voltage-gated sodium channel activity / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / response to corticosterone / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / neuromuscular process / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / sodium ion transport / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / fibroblast growth factor binding / odontogenesis of dentin-containing tooth / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / intercalated disc / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / lateral plasma membrane / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / sodium channel regulator activity / membrane depolarization
Similarity search - Function
iswi atpase / Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate ...iswi atpase / Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Cytokine IL1/FGF / Voltage-gated cation channel calcium and sodium / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Fibroblast growth factor 12 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsWang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S.
CitationJournal: Nat Commun / Year: 2014
Title: Structural analyses of Ca(2+)/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation.
Authors: Wang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor 12
C: Calmodulin
D: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2887
Polymers66,1283
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-73 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.200, 115.200, 120.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Fibroblast growth factor 12 / FGF-12 / Fibroblast growth factor homologous factor 1 / FHF-1 / Myocyte-activating factor


Mass: 27444.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF12, FGF12B, FHF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61328
#2: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Protein Sodium channel protein type 5 subunit alpha / HH1 / Sodium channel protein cardiac muscle subunit alpha / Sodium channel protein type V subunit ...HH1 / Sodium channel protein cardiac muscle subunit alpha / Sodium channel protein type V subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.5


Mass: 21830.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN5A / Production host: Escherichia coli (E. coli) / References: UniProt: Q14524
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7.5
Details: 20% PEG3350, 0.18 M MgSO4, 0.1 M sodium iodide, and CaCl2, pH 7.5, EVAPORATION, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2012
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.83→46.068 Å / Num. all: 3705 / Num. obs: 3705 / % possible obs: 40.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.8-3.87113.2
3.87-3.94118.6
3.94-4.01118.1
4.01-4.09122.3
4.09-4.18122.5
4.18-4.2122.8
4.2-4.39124.8
4.39-4.5126
4.5-4.64128.4
4.64-4.79130.7
4.79-4.96135.6
4.96-5.16137
5.16-5.39141.1
5.39-5.67145.3
5.67-6.03155.8
6.03-6.49171.2
6.49-7.15195
7.15-8.181100
8.18-10.29199.4
10.29-50198.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(AutoMR: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AutoMR: 1.8_1069)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.84→41.57 Å / SU ML: 0.61 / σ(F): 1.38 / Phase error: 35.4 / Stereochemistry target values: ML
Details: THE DIFFRACTION DATA IS HEAVILY ANISOTROPIC (3.8/5.4/6.0 A). AFTER ANISOTROPIC SCALING, THE MODEL REFINES MUCH BETTER WITH INCLUSION OF HIGH-RESOLUTION REFLECTIONS RATHER THAN CUTTING THE ...Details: THE DIFFRACTION DATA IS HEAVILY ANISOTROPIC (3.8/5.4/6.0 A). AFTER ANISOTROPIC SCALING, THE MODEL REFINES MUCH BETTER WITH INCLUSION OF HIGH-RESOLUTION REFLECTIONS RATHER THAN CUTTING THE DATA TO THE LOW RESOLUTION. (6.0 A). ANISOTROPY ALSO GIVES RISE TO THE LOW DATA COMPLETENESS.
RfactorNum. reflection% reflection
Rfree0.3199 202 5.46 %
Rwork0.2534 --
obs0.2571 3700 40.53 %
all-3700 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.84→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 4 0 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013013
X-RAY DIFFRACTIONf_angle_d0.9794114
X-RAY DIFFRACTIONf_dihedral_angle_d11.328988
X-RAY DIFFRACTIONf_chiral_restr0.057492
X-RAY DIFFRACTIONf_plane_restr0.003545
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)
11.7815-0.18710.63241.5602-0.8560.9149-0.0119-0.46980.1608-0.08641.16060.64740.4262-0.04111.88880.90150.8652-0.76731.14220.2737-0.4898-82.125449.3693-49.3605
22.68240.88061.93841.06720.91812.7329-0.18530.57870.3978-0.3667-0.05340.463-0.22340.0039-0.06381.31240.7139-0.42311.0310.18961.1368-82.665854.2479-36.903
31.0504-0.27460.61971.0423-1.161.6072-0.6592-0.62110.5290.66450.0874-0.09380.46030.3266-0.81730.82321.3429-0.80571.91160.12110.2734-72.581446.1915-42.5207
41.12920.0885-0.38070.4732-0.07840.20380.1481-0.65870.40630.5836-0.61040.4980.5959-0.3569-0.5251.2693-0.27670.8622.2449-0.35470.6307-69.254221.4254-94.6687
55.3651-2.72251.7761.5496-0.96590.66990.3018-0.8103-0.54540.30570.25520.45990.9801-0.2492-0.16421.2935-0.33840.28362.2940.22991.8511-83.493422.608-89.457
65.6747-5.75633.01116.2537-1.9714.73980.3166-0.1782-0.14740.20580.11280.0742-0.4285-0.1891-0.11021.64950.271-0.09711.93970.64071.8447-83.773631.2611-81.0886
71.0076-0.03260.6671.83160.50330.6787-0.3058-0.56170.2293-0.88050.14820.4923-0.2813-0.39060.17590.378-0.37010.14611.9256-0.0470.7716-67.009430.9645-80.5006
84.87320.2349-4.40133.155-0.22784.5254-0.2994-0.5096-0.62920.11930.37641.6229-0.3036-1.7201-0.10661.76770.0318-0.68290.9542-0.0271.4163-66.744423.7008-61.3248
98.85335.01994.80076.1883-0.73446.1785-0.1220.787-1.1016-0.69440.10050.11561.2786-0.1751-0.07220.85730.22630.32851.52490.29670.9056-73.060229.5012-67.7038
102.69530.3834-2.79334.343-1.85995.74710.0849-0.23-0.724-0.37950.38780.2280.50160.5864-0.04920.96850.5163-0.06082.259-0.34521.5205-62.451717.5082-68.7826
110.13070.04340.6490.01410.21056.5614-0.27080.87430.6456-0.3487-0.0829-0.273-0.77360.17870.38960.6021-0.266-0.53082.1490.34011.7035-47.934158.3729-59.379
120.9650.33021.07492.56210.21281.2033-0.38290.30380.7275-0.0894-0.4936-0.3204-0.1797-0.0896-0.76450.3056-0.2069-0.31391.80320.22730.5885-51.126145.7228-61.8851
130.36120.6362-0.54575.4989-1.40272.0755-0.02640.6399-0.20140.07950.2256-0.13880.21-0.0445-0.00590.74640.7162-0.72251.7208-0.13531.5191-57.835549.5958-55.3423
140.84690.52040.43810.29970.32460.3403-0.5224-0.63551.15841.06860.07980.145-1.32510.2896-0.03071.91810.4130.00611.86970.05691.1848-57.990657.041-48.4484
150.0327-0.0746-0.02040.20460.0210.12920.09630.3215-0.7308-0.85670.17250.42670.33820.0743-0.12961.0212-0.25520.16430.5125-0.35871.5984-66.728727.1125-75.8013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 152 )
4X-RAY DIFFRACTION4chain 'C' and (resid 7 through 20 )
5X-RAY DIFFRACTION5chain 'C' and (resid 21 through 40 )
6X-RAY DIFFRACTION6chain 'C' and (resid 41 through 56 )
7X-RAY DIFFRACTION7chain 'C' and (resid 57 through 99 )
8X-RAY DIFFRACTION8chain 'C' and (resid 100 through 112 )
9X-RAY DIFFRACTION9chain 'C' and (resid 113 through 118 )
10X-RAY DIFFRACTION10chain 'C' and (resid 119 through 148 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1786 through 1807 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1808 through 1837 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1838 through 1862 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1863 through 1895 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1896 through 1927 )

+
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