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- PDB-7spd: Crystal Structure of The Tetramerization Domain (29-147) From Hum... -

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Basic information

Entry
Database: PDB / ID: 7spd
TitleCrystal Structure of The Tetramerization Domain (29-147) From Human Voltage-gated Potassium Channel Kv2.1 in C 2 2 21 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 / 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
Potassium channel, voltage dependent, Kv2.1 / Voltage-gated potassium channel / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily ...Potassium channel, voltage dependent, Kv2.1 / Voltage-gated potassium channel / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Potassium voltage-gated channel subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXu, Z. / Schnicker, N. / Baker, S.
Funding support2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY0202542
Other privateBR-CMM-0619-0763-UIA
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
DepositionNov 2, 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)74,28217
Polymers73,2525
Non-polymers1,02912
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-110 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.290, 114.120, 112.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11D-204-

ZN

21B-205-

HOH

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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: tetramerization domain (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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M magnesium chloride, 15% PEG400, 0.1 M HEPES, pH 7.5

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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 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.43 Å / Num. obs: 36640 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 56.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.045 / Rrim(I) all: 0.122 / Net I/σ(I): 17.2
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
2.7-2.836.71.2921690125340.6380.5371.41.5100
8.96-48.436.60.02539235920.9990.010.02859.599.4

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Processing

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

3kvt


Resolution: 2.7→45.67 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 1982 5.41 %
Rwork0.2116 34658 -
obs0.2136 36640 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.11 Å2 / Biso mean: 58.5066 Å2 / Biso min: 29.82 Å2
Refinement stepCycle: final / Resolution: 2.7→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 98 13 4312
Biso mean--70.93 51.32 -
Num. residues----532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.770.37041480.319224722620
2.77-2.840.30481310.304624792610
2.84-2.930.33761370.287124832620
2.93-3.020.31961830.264624332616
3.02-3.130.30951620.258124662628
3.13-3.250.2321540.225324632617
3.25-3.40.34131480.248824512599
3.4-3.580.25441150.205225142629
3.58-3.810.27971330.20224722605
3.81-4.10.24371490.198724742623
4.1-4.510.20511010.180625002601
4.51-5.160.191460.177324952641
5.16-6.50.22381290.197724882617
6.5-45.670.20611460.192624682614

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