[English] 日本語
Yorodumi
- PDB-4dck: Crystal structure of the C-terminus of voltage-gated sodium chann... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dck
TitleCrystal structure of the C-terminus of voltage-gated sodium channel in complex with FGF13 and CaM
Components
  • Calmodulin
  • Fibroblast growth factor 13
  • Sodium channel protein type 5 subunit alpha
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / IQ-motif / EF-hand / Voltage-gated Sodium Channel regulation / Nav1.5 CTD binds to FGF13 and CaM. CaM binds to Ca2+. / TRANSPORT PROTEIN-TRANSPORT PROTEIN REGULATOR-SIGNALING PROTEIN complex / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


establishment of neuroblast polarity / 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 SA node cell action potential / bundle of His cell action potential / AV node cell action potential / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / AV node cell to bundle of His cell communication / negative regulation of collateral sprouting ...establishment of neuroblast polarity / 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 SA node cell action potential / bundle of His cell action potential / AV node cell action potential / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / AV node cell to bundle of His cell communication / negative regulation of collateral sprouting / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation / positive regulation of voltage-gated sodium channel activity / cardiac ventricle development / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / branching morphogenesis of a nerve / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / regulation of sodium ion transmembrane transport / brainstem development / membrane depolarization during AV node cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during bundle of His cell action potential / positive regulation of action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / telencephalon development / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / : / inhibitory synapse assembly / establishment of protein localization to mitochondrial membrane / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / type 3 metabotropic glutamate receptor binding / negative regulation of microtubule depolymerization / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of cardiac muscle cell contraction / voltage-gated sodium channel complex / membrane depolarization during action potential / Interaction between L1 and Ankyrins / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / voltage-gated sodium channel activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ankyrin binding / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / sodium ion transport / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / fibroblast growth factor binding / beta-tubulin binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / cerebral cortex cell migration / odontogenesis of dentin-containing tooth / microtubule polymerization / RHO GTPases activate PAKs / membrane depolarization / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / intercalated disc / DARPP-32 events / detection of calcium ion / sodium ion transmembrane transport
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 / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / HBGF/FGF family signature. / Voltage gated sodium channel, alpha subunit / Fibroblast growth factor family ...iswi atpase / Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / HBGF/FGF family signature. / Voltage gated sodium channel, alpha subunit / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / 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 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha / Fibroblast growth factor 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChung, B.C. / Wang, C. / Yan, H. / Pitt, G.S. / Lee, S.Y.
CitationJournal: Structure / Year: 2012
Title: Crystal Structure of the Ternary Complex of a NaV C-Terminal Domain, a Fibroblast Growth Factor Homologous Factor, and Calmodulin.
Authors: Wang, C. / Chung, B.C. / Yan, H. / Lee, S.Y. / Pitt, G.S.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Feb 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.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_asym_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: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9056
Polymers57,8323
Non-polymers733
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-43 kcal/mol
Surface area22480 Å2
MethodPISA
2
A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules

A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules

A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,71518
Polymers173,4969
Non-polymers2199
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area20840 Å2
ΔGint-178 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.041, 126.041, 126.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-362-

HOH

DetailsThe C-terminus of voltage-gated sodium channel is a monomer and in complex with FGF13 and CaM. So it is heterotrimer (ternary complex).

-
Components

#1: 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: 19369.891 Da / Num. of mol.: 1 / Fragment: C-terminal domain of Nav1.5
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
#2: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1 / Fragment: Calmodulin
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 Fibroblast growth factor 13 / FGF-13 / Fibroblast growth factor homologous factor 2 / FHF-2


Mass: 21609.592 Da / Num. of mol.: 1 / Fragment: FGF13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF13, FHF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92913
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG400, 150mM Magnesium Acetate, 50mM Sodium Cacodylate , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 24-ID-C21
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDAug 1, 2011
ADSC QUANTUM 3152CCDAug 22, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal, Si 111SINGLE WAVELENGTHMx-ray1
2double crystal, Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33622 / Num. obs: 33622 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 39.3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.21-2.251,294.8
2.25-2.291,297
2.29-2.341,298.5
2.34-2.41,298.5
2.4-2.461,298.9
2.46-2.531,298.5
2.53-2.61,299
2.6-2.681,299.4
2.68-2.781,299.4
2.78-2.891,299.5
2.89-3.021,299.6
3.02-3.181,299.8
3.18-3.381,299.8
3.38-3.641,299.9
3.64-4.011,299.9
4.01-4.591,299.9
4.59-5.781,2100
5.78-501,299.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.reflection_file_editor: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.858 Å / SU ML: 0.48 / σ(F): 1.44 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1701 5 %Random
Rwork0.2098 ---
obs0.2107 -99.76 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.578 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 3 202 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113563
X-RAY DIFFRACTIONf_angle_d0.8234798
X-RAY DIFFRACTIONf_dihedral_angle_d14.4861343
X-RAY DIFFRACTIONf_chiral_restr0.056521
X-RAY DIFFRACTIONf_plane_restr0.004622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.26480.26381400.26252641X-RAY DIFFRACTION99
2.2648-2.33790.28441410.24552656X-RAY DIFFRACTION100
2.3379-2.42150.25181400.23492657X-RAY DIFFRACTION100
2.4215-2.51840.25581400.23222693X-RAY DIFFRACTION100
2.5184-2.6330.31091440.2412665X-RAY DIFFRACTION100
2.633-2.77180.26361380.23912673X-RAY DIFFRACTION100
2.7718-2.94540.2411430.23562679X-RAY DIFFRACTION100
2.9454-3.17270.24511390.23522692X-RAY DIFFRACTION100
3.1727-3.49190.2521430.21662701X-RAY DIFFRACTION100
3.4919-3.99670.20661430.19862705X-RAY DIFFRACTION100
3.9967-5.03390.18021400.17242746X-RAY DIFFRACTION100
5.0339-39.86420.21761500.19952818X-RAY DIFFRACTION100

+
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