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- PDB-7re5: Crystal Structure of The Tetramerization Domain (29-147) From Hum... -
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Basic information
Entry | Database: PDB / ID: 7re5 | |||||||||
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Title | Crystal Structure of The Tetramerization Domain (29-147) From Human Voltage-gated Potassium Channel Kv2.1 in P 41 21 2 Space Group | |||||||||
![]() | Potassium voltage-gated channel subfamily B member 1 | |||||||||
![]() | SIGNALING PROTEIN / Pentamer / potassium voltage-gated channel / T1 domain | |||||||||
Function / homology | ![]() regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / potassium ion export across plasma membrane / proximal dendrite / : / positive regulation of calcium ion-dependent exocytosis ...regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / potassium ion export across plasma membrane / proximal dendrite / : / positive regulation of calcium ion-dependent exocytosis / Voltage gated Potassium channels / delayed rectifier potassium channel activity / glutamate receptor signaling pathway / outward rectifier potassium channel activity / vesicle docking involved in exocytosis / regulation of monoatomic ion transmembrane transport / anchoring junction / response to L-glutamate / action potential / neuronal cell body membrane / voltage-gated potassium channel activity / cellular response to nutrient levels / lateral plasma membrane / response to axon injury / positive regulation of protein targeting to membrane / negative regulation of insulin secretion / potassium ion transmembrane transport / voltage-gated potassium channel complex / dendrite membrane / cellular response to calcium ion / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / protein homooligomerization / sarcolemma / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / postsynaptic membrane / perikaryon / transmembrane transporter binding / membrane => GO:0016020 / apical plasma membrane / protein heterodimerization activity / axon / dendrite / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, Z. / Schnicker, N. / Baker, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Pentameric assembly of the Kv2.1 tetramerization domain. Authors: Xu, Z. / Khan, S. / Schnicker, N.J. / Baker, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.3 KB | Display | ![]() |
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PDB format | ![]() | 92.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7spdC ![]() 3kvtS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14650.493 Da / Num. of mol.: 5 / Fragment: UNP residues 29-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris, pH 8.5, 3.4 M 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: May 5, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07216 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→44.37 Å / Num. obs: 44658 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 48.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.027 / Rrim(I) all: 0.1 / Net I/σ(I): 26.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3KVT Resolution: 2.5→44.37 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.04 Å2 / Biso mean: 51.8948 Å2 / Biso min: 22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→44.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %
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