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- PDB-1s6c: Crystal structure of the complex between KChIP1 and Kv4.2 N1-30 -

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Basic information

Entry
Database: PDB / ID: 1s6c
TitleCrystal structure of the complex between KChIP1 and Kv4.2 N1-30
Components
  • Kv4 potassium channel-interacting protein KChIP1b
  • Potassium voltage-gated channel subfamily D member 2
KeywordsTRANSPORT PROTEIN / EF-hand
Function / homology
Function and homology information


Phase 1 - inactivation of fast Na+ channels / cardiac muscle cell action potential / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / : / perinuclear endoplasmic reticulum / positive regulation of action potential ...Phase 1 - inactivation of fast Na+ channels / cardiac muscle cell action potential / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / : / perinuclear endoplasmic reticulum / positive regulation of action potential / membrane repolarization / voltage-gated monoatomic ion channel activity / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / anchoring junction / action potential / neuronal cell body membrane / voltage-gated potassium channel activity / potassium channel activity / plasma membrane raft / locomotor rhythm / GABA-ergic synapse / potassium channel regulator activity / neuronal action potential / potassium ion transmembrane transport / voltage-gated potassium channel complex / extrinsic component of cytoplasmic side of plasma membrane / sensory perception of pain / T-tubule / caveola / muscle contraction / potassium ion transport / protein homooligomerization / sarcolemma / cellular response to mechanical stimulus / cellular response to xenobiotic stimulus / monoatomic ion channel activity / cellular response to hypoxia / postsynaptic membrane / perikaryon / transmembrane transporter binding / dendritic spine / neuronal cell body / glutamatergic synapse / calcium ion binding / dendrite / protein-containing complex binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.2 / 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) / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain ...Potassium channel, voltage dependent, Kv4.2 / 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) / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / EF-hand domain pair / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / EF-hand / Recoverin; domain 1 / SKP1/BTB/POZ domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily D member 2 / Kv channel-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, W. / Qian, Y. / Kunjilwar, K. / Pfaffinger, P.J. / Choe, S.
CitationJournal: Neuron / Year: 2004
Title: Structural insights into the functional interaction of KChIP1 with Shal-type K(+) channels.
Authors: Zhou, W. / Qian, Y. / Kunjilwar, K. / Pfaffinger, P.J. / Choe, S.
History
DepositionJan 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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

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Assembly

Deposited unit
A: Kv4 potassium channel-interacting protein KChIP1b
B: Potassium voltage-gated channel subfamily D member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8084
Polymers24,7282
Non-polymers802
Water2,702150
1
A: Kv4 potassium channel-interacting protein KChIP1b
B: Potassium voltage-gated channel subfamily D member 2
hetero molecules

A: Kv4 potassium channel-interacting protein KChIP1b
B: Potassium voltage-gated channel subfamily D member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6168
Polymers49,4564
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area8380 Å2
ΔGint-131 kcal/mol
Surface area15950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.744, 74.487, 85.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Kv4 potassium channel-interacting protein KChIP1b


Mass: 21760.275 Da / Num. of mol.: 1 / Fragment: Core domain (Residues 34-216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: KChIP1 / Plasmid: pHIS8 (pET28_mod) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (ED3) / References: UniProt: Q8R426
#2: Protein/peptide Potassium voltage-gated channel subfamily D member 2 / Potassium channel Kv4.2 / Shal1 / RK5


Mass: 2967.552 Da / Num. of mol.: 1 / Fragment: N-terminus (Residues 1-30)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: KCND2 / Plasmid: pHIS8 (pET28_mod) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q63881
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1000, magnesium nitrate, sodium cacodylate, DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
25 mMTris1droppH8.0
350 mM1dropNaCl
4100 mMsodium cacodylate1reservoirpH6.0
5100 mM1reservoirMgNO3
620 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.044 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2002
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 16062 / Num. obs: 16062 / % possible obs: 97.5 %
Reflection shellResolution: 2→2.07 Å / % possible all: 94.76
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 148552 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 94.8 % / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G8I

1g8i


Resolution: 2→19.79 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 808 RANDOM
Rwork0.206 --
all-16042 -
obs-16042 -
Refinement stepCycle: LAST / Resolution: 2→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 2 150 1667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_bond_d0.05
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.272

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