[English] 日本語
Yorodumi- PDB-2kxw: Structure of the C-domain Fragment of apo Calmodulin Bound to the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kxw | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the C-domain Fragment of apo Calmodulin Bound to the IQ motif of Nav1.2 | ||||||
Components |
| ||||||
Keywords | CALCIUM-BINDING PROTEIN/METAL TRANSPORT / Action Potential / Amino Acid Motifs / Animals / Autism / Biomolecular / Brain Chemistry / Calcium-Binding Proteins / Calmodulin / Channel / Glutamine / Humans / Ion Channel Gating / Isoleucine / IQ Motif / Metal Transport / Models / Molecular / NaV1.2 / Neuronal / Peptides / Protein Binding / Protein Structure / Sodium Channels / Tertiary / Tyrosine / Voltage-Dependent / Voltage Gated / CALCIUM-BINDING PROTEIN-METAL TRANSPORT complex | ||||||
Function / homology | Function and homology information leucine zipper domain binding / axon initial segment / sodium ion binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dentate gyrus development / node of Ranvier ...leucine zipper domain binding / axon initial segment / sodium ion binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dentate gyrus development / node of Ranvier / voltage-gated sodium channel complex / membrane depolarization during action potential / optic nerve development / voltage-gated sodium channel activity / sodium ion transport / axon development / intercalated disc / sodium ion transmembrane transport / neuronal action potential / enzyme regulator activity / T-tubule / myelination / determination of adult lifespan / cerebral cortex development / memory / presynaptic membrane / nervous system development / cellular response to hypoxia / neuron apoptotic process / calmodulin binding / axon / glutamatergic synapse / calcium ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Paramecium tetraurelia (eukaryote) Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | minimized average, model 1 | ||||||
Authors | Feldkamp, M.D. / Yu, L. / Shea, M.A. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structural and Energetic Determinants of Apo Calmodulin Binding to the IQ Motif of the Na(V)1.2 Voltage-Dependent Sodium Channel. Authors: Feldkamp, M.D. / Yu, L. / Shea, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2kxw.cif.gz | 675.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2kxw.ent.gz | 564.1 KB | Display | PDB format |
PDBx/mmJSON format | 2kxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kxw_validation.pdf.gz | 355.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2kxw_full_validation.pdf.gz | 603.7 KB | Display | |
Data in XML | 2kxw_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 2kxw_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/2kxw ftp://data.pdbj.org/pub/pdb/validation_reports/kx/2kxw | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8416.313 Da / Num. of mol.: 1 / Fragment: C-domain (UNP Residues 77-149) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Gene: CAM, GSPATT00015825001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 DE3 / References: UniProt: P07463 |
---|---|
#2: Protein/peptide | Mass: 3370.088 Da / Num. of mol.: 1 Fragment: IQ-motif of the Voltage-dependent Sodium Channel (UNP Residues 1901-1927) Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P04775 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions | Ionic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||
NMR constraints | NOE constraints total: 1819 / NOE intraresidue total count: 457 / NOE long range total count: 331 / NOE medium range total count: 300 / NOE sequential total count: 298 / Hydrogen bond constraints total count: 46 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54 | ||||||||||||||||
NMR representative | Selection criteria: energy minimized average structure | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 300 / Conformers submitted total number: 21 / Maximum lower distance constraint violation: 0.005 Å / Maximum upper distance constraint violation: 0.016 Å | ||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.008 Å / Distance rms dev error: 0.001 Å |