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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
TitleCrystal Structure of The Tetramerization Domain (29-147) From Human Voltage-gated Potassium Channel Kv2.1 in P 41 21 2 Space Group
ComponentsPotassium voltage-gated channel subfamily B member 1
KeywordsSIGNALING PROTEIN / Pentamer / potassium voltage-gated channel / T1 domain
Function / homology
Function and homology information


regulation of action potential / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / cholinergic synapse / potassium ion export across plasma membrane / positive regulation of calcium ion-dependent exocytosis / delayed rectifier potassium channel activity ...regulation of action potential / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / cholinergic synapse / potassium ion export across plasma membrane / positive regulation of calcium ion-dependent exocytosis / delayed rectifier potassium channel activity / proximal dendrite / Voltage gated Potassium channels / outward rectifier potassium channel activity / vesicle docking involved in exocytosis / response to L-glutamate / postsynaptic specialization membrane / neuronal cell body membrane / glutamate receptor signaling pathway / action potential / lateral plasma membrane / positive regulation of protein targeting to membrane / potassium channel regulator activity / response to axon injury / cellular response to nutrient levels / voltage-gated potassium channel complex / potassium ion transmembrane transport / dendrite membrane / cellular response to calcium ion / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / negative regulation of insulin secretion / sarcolemma / protein homooligomerization / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / perikaryon / transmembrane transporter binding / postsynaptic membrane / apical plasma membrane / protein heterodimerization activity / axon / dendrite / perinuclear region of cytoplasm / cell surface / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain ...Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXu, Z. / Schnicker, N. / Baker, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY0202542 United States
Foundation Fighting BlindnessBR-CMM-0619-0763-UIA United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Pentameric assembly of the Kv2.1 tetramerization domain.
Authors: Xu, Z. / Khan, S. / Schnicker, N.J. / Baker, S.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily B member 1
B: Potassium voltage-gated channel subfamily B member 1
C: Potassium voltage-gated channel subfamily B member 1
D: Potassium voltage-gated channel subfamily B member 1
E: Potassium voltage-gated channel subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,77613
Polymers73,2525
Non-polymers5238
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, The SAXS profile of Kv2.1 T1 has a good agreement with the pentameric conformation of the crystal structure coordinates., light scattering, Molecular Weight determined by Multiple ...Evidence: SAXS, The SAXS profile of Kv2.1 T1 has a good agreement with the pentameric conformation of the crystal structure coordinates., light scattering, Molecular Weight determined by Multiple Angle Light Scattering is 72 kDa., electron microscopy, Top View of Pentameric state is verified by Negative Stain
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-220 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.754, 78.754, 214.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

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Components

#1: Protein
Potassium voltage-gated channel subfamily B member 1 / Delayed rectifier potassium channel 1 / DRK1 / h-DRK1 / Voltage-gated potassium channel subunit Kv2.1


Mass: 14650.493 Da / Num. of mol.: 5 / Fragment: UNP residues 29-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14721
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07216 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.613.11.1083533126960.8370.3161.1532.5100
9.01-44.3711.70.031739863410.0090.03277.599.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.7.4data scaling
Coot0.9.5model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KVT

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
RfactorNum. reflection% reflection
Rfree0.2675 2227 4.99 %
Rwork0.2252 42431 -
obs0.2273 44658 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.04 Å2 / Biso mean: 51.8948 Å2 / Biso min: 22 Å2
Refinement stepCycle: final / Resolution: 2.5→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 8 25 4349
Biso mean--70.98 46.09 -
Num. residues----542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.550.37561310.317526602791
2.55-2.610.40391340.304926762810
2.61-2.680.43561330.310126412774
2.68-2.750.35911490.294226512800
2.75-2.830.40041460.29326622808
2.83-2.920.33321740.291126272801
2.92-3.030.32741460.258826352781
3.03-3.150.3011160.267826842800
3.15-3.290.36271440.263326162760
3.29-3.470.26881420.243726612803
3.47-3.680.27021230.209326602783
3.68-3.970.29391350.211126812816
3.97-4.370.17561490.192426162765
4.37-50.19091570.17526282785
5-6.290.24171160.19826662782
6.3-44.370.21931320.191826672799

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