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- PDB-1s1g: Crystal Structure of Kv4.3 T1 Domain -

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Basic information

Entry
Database: PDB / ID: 1s1g
TitleCrystal Structure of Kv4.3 T1 Domain
ComponentsPotassium voltage-gated channel subfamily D member 3
KeywordsTRANSPORT PROTEIN / K+ channels / tetramerization domain / T1 domain
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / membrane repolarization / Voltage gated Potassium channels / postsynaptic specialization membrane / regulation of heart rate by cardiac conduction ...ventricular cardiac muscle cell membrane repolarization / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / membrane repolarization / Voltage gated Potassium channels / postsynaptic specialization membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / GABA-ergic synapse / voltage-gated potassium channel complex / sarcolemma / protein homooligomerization / potassium ion transport / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / metal ion binding / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A ...Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily D member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsScannevin, R.H. / Wang, K.W. / Jow, F. / Megules, J. / Kopsco, D.C. / Edris, W. / Carroll, K.C. / Lu, Q. / Xu, W.X. / Xu, Z.B. ...Scannevin, R.H. / Wang, K.W. / Jow, F. / Megules, J. / Kopsco, D.C. / Edris, W. / Carroll, K.C. / Lu, Q. / Xu, W.X. / Xu, Z.B. / Katz, A.H. / Olland, S. / Lin, L. / Taylor, M. / Stahl, M. / Malakian, K. / Somers, W. / Mosyak, L. / Bowlby, M.R. / Chanda, P. / Rhodes, K.J.
CitationJournal: Neuron / Year: 2004
Title: Two N-terminal domains of Kv4 K(+) channels regulate binding to and modulation by KChIP1.
Authors: Scannevin, R.H. / Wang, K.W. / Jow, F. / Megules, J. / Kopsco, D.C. / Edris, W. / Carroll, K.C. / Xu, W.X. / Xu, Z.B. / Katz, A.H. / Olland, S. / Lin, L. / Taylor, M. / Stahl, M. / Malakian, ...Authors: Scannevin, R.H. / Wang, K.W. / Jow, F. / Megules, J. / Kopsco, D.C. / Edris, W. / Carroll, K.C. / Xu, W.X. / Xu, Z.B. / Katz, A.H. / Olland, S. / Lin, L. / Taylor, M. / Stahl, M. / Malakian, K. / Somers, W. / Mosyak, L. / Bowlby, M.R. / Chanda, P. / Rhodes, K.J.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 D member 3
B: Potassium voltage-gated channel subfamily D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4474
Polymers30,3162
Non-polymers1312
Water50428
1
A: Potassium voltage-gated channel subfamily D member 3
B: Potassium voltage-gated channel subfamily D member 3
hetero molecules

A: Potassium voltage-gated channel subfamily D member 3
B: Potassium voltage-gated channel subfamily D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8938
Polymers60,6324
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7240 Å2
ΔGint-165 kcal/mol
Surface area19690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.230, 84.230, 104.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Potassium voltage-gated channel subfamily D member 3 / Potassium channel Kv4.3


Mass: 15157.938 Da / Num. of mol.: 2 / Fragment: Kv4.3T1 (residue 29-143, SWS Q9Uk17)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCND3 / Plasmid: pET-21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9UK17
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.55 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10.6
Details: Sodium Phosphate/Potassium Phosphate, Lisium Sulfate, CAPS, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-7 mg/mlprotein1drop
225 mMTris1droppH7.4
3100 mM1dropNaCl
410 mMdithiothreitol1drop
51 mM1dropZnCl2
62.0 Mpotassium sodium phosphate1reservoir
70.2 M1reservoirLi2SO4
80.1 MCAPS1reservoirpH10.5

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Data collection

DiffractionMean temperature: 143 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 12111 / Num. obs: 12263 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.071
Reflection shellResolution: 2.6→2.69 Å / Num. unique all: 995 / % possible all: 87

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 3kvt

3kvt


Resolution: 2.6→19.85 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 160298.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 599 5.1 %RANDOM
Rwork0.228 ---
all0.23 11641 --
obs0.228 11641 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2124 Å2 / ksol: 0.367987 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 2 28 1903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 38 3.7 %
Rwork0.324 995 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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