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- PDB-2nz0: Crystal structure of potassium channel Kv4.3 in complex with its ... -

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Basic information

Entry
Database: PDB / ID: 2nz0
TitleCrystal structure of potassium channel Kv4.3 in complex with its regulatory subunit KChIP1
Components
  • Kv channel-interacting protein 1
  • Potassium voltage-gated channel subfamily D member 3
KeywordsMEMBRANE PROTEIN / Kv4.3 / KChIP1
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / Kv4.3-KChIP1 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport ...ventricular cardiac muscle cell membrane repolarization / Kv4.3-KChIP1 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / regulation of heart contraction / regulation of heart rate by cardiac conduction / action potential / voltage-gated potassium channel activity / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / GABA-ergic synapse / muscle contraction / potassium ion transmembrane transport / protein tetramerization / potassium ion transport / protein homooligomerization / sarcolemma / cytoplasmic side of plasma membrane / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / dendrite / calcium ion binding / synapse / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain ...Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Recoverin family / 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
A-type potassium channel modulatory protein KCNIP1 / A-type voltage-gated potassium channel KCND3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, H. / Yan, Y. / Shen, Y. / Chen, L. / Wang, K.
CitationJournal: Nat.Neurosci. / Year: 2007
Title: Structural basis for modulation of Kv4 K(+) channels by auxiliary KChIP subunits.
Authors: Wang, H. / Yan, Y. / Liu, Q. / Huang, Y. / Shen, Y. / Chen, L. / Chen, Y. / Yang, Q. / Hao, Q. / Wang, K. / Chai, J.
History
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.title / _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: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,74810
Polymers75,4574
Non-polymers2916
Water00
1
A: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules

A: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,49720
Polymers150,9148
Non-polymers58212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area24390 Å2
ΔGint-368 kcal/mol
Surface area57550 Å2
MethodPISA
2
A: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules

A: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules

A: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules

A: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,99340
Polymers301,82916
Non-polymers1,16524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)112.186, 112.213, 141.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a heteroctamer generated from the heterodimer of Kv4.3 and KChIP1 (A and B molecules) in the asymmetric unit by the operations: -X, -Y, Z as well as the heterodimer of Kv4.3 and KChIP1 (C and D molecules) by the operations: -X+1/2, Y+1/2, -Z+1/2 and X+1/2, -Y+1/2, -Z+1/2

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Components

#1: Protein Kv channel-interacting protein 1 / KChIP1 / A-type potassium channel modulatory protein 1 / Potassium channel-interacting protein 1 / ...KChIP1 / A-type potassium channel modulatory protein 1 / Potassium channel-interacting protein 1 / Vesicle APC-binding protein


Mass: 21147.908 Da / Num. of mol.: 2 / Fragment: N-terminal deletion domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KChIP1 / Plasmid: pET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZI2
#2: Protein Potassium voltage-gated channel subfamily D member 3 / Voltage-gated potassium channel subunit Kv4.3


Mass: 16580.711 Da / Num. of mol.: 2 / Fragment: N-terminal domain (residues 6-145)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: K-12 / Gene: Kv4.3 / Plasmid: pET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UK17
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 2.0 M NaH2PO4/K2HPO4, 0.2 M Li2SO4 and 0.1 M CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→99 Å / Num. all: 15065 / Num. obs: 14680 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.489 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.891 / SU B: 67.057 / SU ML: 0.538 / Cross valid method: THROUGHOUT / ESU R Free: 0.628 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31015 1114 7.6 %RANDOM
Rwork0.26082 ---
obs0.26458 13587 97.92 %-
all-13547 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.965 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2--2.39 Å20 Å2
3----5.77 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 6 0 5084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.9487030
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7995606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01824.097288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78615896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4161536
X-RAY DIFFRACTIONr_chiral_restr0.060.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024064
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.22365
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23623
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.2157
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4431.53129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79124936
X-RAY DIFFRACTIONr_scbond_it0.82232353
X-RAY DIFFRACTIONr_scangle_it1.3974.52094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.371 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.407 176 -
Rwork0.347 1911 -
obs--98.68 %

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