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- PDB-3wfn: Crystal Structure of Nav1.6 IQ motif in complex with apo-CaM -

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Basic information

Entry
Database: PDB / ID: 3wfn
TitleCrystal Structure of Nav1.6 IQ motif in complex with apo-CaM
ComponentsCalmodulin, Sodium channel protein type 8 subunit alpha
KeywordsMETAL BINDING PROTEIN / EF-hand motif / Calcium binding protein / IQ motif
Function / homology
Function and homology information


negative regulation of calcium ion transmembrane transporter activity / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation ...negative regulation of calcium ion transmembrane transporter activity / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Reduction of cytosolic Ca++ levels / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / Calcineurin activates NFAT / Ion transport by P-type ATPases / RAF activation / sodium channel complex / VEGFR2 mediated vascular permeability / RAS processing / Ca2+ pathway / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / sodium ion binding / nerve development / Smooth Muscle Contraction / : / : / : / : / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / : / Stimuli-sensing channels / establishment of protein localization to mitochondrial membrane / Ion homeostasis / type 3 metabotropic glutamate receptor binding / node of Ranvier / voltage-gated sodium channel complex / adult walking behavior / podosome / anchoring junction / voltage-gated sodium channel activity / response to corticosterone / negative regulation of high voltage-gated calcium channel activity / muscle organ development / sodium ion transport / negative regulation of ryanodine-sensitive calcium-release channel activity / 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 / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / catalytic complex / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / postsynaptic cytosol / activation of adenylate cyclase activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / regulation of heart rate / calyx of Held / response to amphetamine / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / locomotory behavior
Similarity search - Function
Voltage gated sodium channel, alpha-8 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / 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 / IQ calmodulin-binding motif / Voltage-gated cation channel calcium and sodium ...Voltage gated sodium channel, alpha-8 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / 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 / IQ calmodulin-binding motif / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Voltage-dependent channel domain superfamily / : / 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
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 / Sodium channel protein type 8 subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChichili, V.P.R. / Sivaraman, J.
CitationJournal: Sci Rep / Year: 2013
Title: Structural Basis for the Modulation of the Neuronal Voltage-Gated Sodium Channel NaV1.6 by Calmodulin
Authors: Chichili, V.P.R. / Xiao, Y. / Seetharaman, J. / Cummins, T.R. / Sivaraman, J.
History
DepositionJul 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Calmodulin, Sodium channel protein type 8 subunit alpha
C: Calmodulin, Sodium channel protein type 8 subunit alpha
D: Calmodulin, Sodium channel protein type 8 subunit alpha
E: Calmodulin, Sodium channel protein type 8 subunit alpha


Theoretical massNumber of molelcules
Total (without water)81,9264
Polymers81,9264
Non-polymers00
Water10,719595
1
B: Calmodulin, Sodium channel protein type 8 subunit alpha


Theoretical massNumber of molelcules
Total (without water)20,4821
Polymers20,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Calmodulin, Sodium channel protein type 8 subunit alpha


Theoretical massNumber of molelcules
Total (without water)20,4821
Polymers20,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Calmodulin, Sodium channel protein type 8 subunit alpha


Theoretical massNumber of molelcules
Total (without water)20,4821
Polymers20,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Calmodulin, Sodium channel protein type 8 subunit alpha


Theoretical massNumber of molelcules
Total (without water)20,4821
Polymers20,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.830, 50.752, 150.666
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Calmodulin, Sodium channel protein type 8 subunit alpha / CaM / Sodium channel protein type VIII subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.6


Mass: 20481.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CHIMERA PROTEIN OF CALMODULIN (UNIPROT P62204 CALM_MOUSE) AND NAV1.6 IQ MOTIF FROM SODIUM CHANNEL PROTEIN TYPE 8 SUBUNIT ALPHA (UNIPROT Q9WTU3 SCN8A_MOUSE, RESIDUES 1893-1914)
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: P62204, UniProt: Q9WTU3, UniProt: P0DP26*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-Tris Propane pH 6.5, 55% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2012
RadiationMonochromator: channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 83450 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 30.6 Å2
Reflection shellHighest resolution: 1.9 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→48.095 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.828 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1828 2.37 %
Rwork0.2003 75280 -
obs0.2011 77108 95.35 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.956 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 118.5 Å2 / Biso mean: 40.7355 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1-9.0587 Å2-0 Å2-3.0241 Å2
2---10.1214 Å20 Å2
3---3.773 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5099 0 0 595 5694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065154
X-RAY DIFFRACTIONf_angle_d0.9526887
X-RAY DIFFRACTIONf_chiral_restr0.072747
X-RAY DIFFRACTIONf_plane_restr0.004919
X-RAY DIFFRACTIONf_dihedral_angle_d14.2531938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.00270.29341330.24775331546489
2.0027-2.06170.27891340.22085406554089
2.0617-2.12820.27561360.20955383551990
2.1282-2.20430.26671340.2095547568191
2.2043-2.29250.27751330.20755664579794
2.2925-2.39690.25161390.20615828596796
2.3969-2.52320.25071490.21025980612999
2.5232-2.68130.26541420.211760176159100
2.6813-2.88830.24041420.21360306172100
2.8883-3.17890.24471530.206461316284100
3.1789-3.63880.23781490.193760546203100
3.6388-4.58390.1831370.16285976611397
4.5839-48.10950.23251470.21425933608094
Refinement TLS params.Method: refined / Origin x: 73.7589 Å / Origin y: -1.2083 Å / Origin z: 37.1033 Å
111213212223313233
T0.1621 Å20.0214 Å2-0.0413 Å2-0.2536 Å2-0.0286 Å2--0.1583 Å2
L-0.0127 °2-0.0191 °2-0.1006 °2-0.4747 °2-0.036 °2---0.0778 °2
S-0.0112 Å °0.0191 Å °-0.0156 Å °0.0147 Å °0.0154 Å °-0.0299 Å °0.0049 Å °0.0163 Å °-0.0029 Å °
Refinement TLS groupSelection details: all

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