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- PDB-3dd4: Structural Basis of KChIP4a Modulation of Kv4.3 Slow Inactivation -

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Basic information

Entry
Database: PDB / ID: 3dd4
TitleStructural Basis of KChIP4a Modulation of Kv4.3 Slow Inactivation
ComponentsKv channel-interacting protein 4
KeywordsTRANSPORT PROTEIN / EF-hands protein / Ion transport / Ionic channel / Membrane / Potassium / Potassium channel / Potassium transport / Transport / Voltage-gated channel
Function / homology
Function and homology information


Phase 1 - inactivation of fast Na+ channels / regulation of potassium ion transmembrane transport / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / protein localization to plasma membrane / peroxisome / neuronal cell body / dendrite / calcium ion binding ...Phase 1 - inactivation of fast Na+ channels / regulation of potassium ion transmembrane transport / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / protein localization to plasma membrane / peroxisome / neuronal cell body / dendrite / calcium ion binding / plasma membrane / cytosol
Similarity search - Function
Recoverin family / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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 ...Recoverin family / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Kv channel-interacting protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChai, J. / Wang, H. / Wang, K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Insights into KChIP4a Modulation of Kv4.3 Inactivation.
Authors: Liang, P. / Wang, H. / Chen, H. / Cui, Y. / Gu, L. / Chai, J. / Wang, K.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 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_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_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_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Kv channel-interacting protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6093
Polymers26,5291
Non-polymers802
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Kv channel-interacting protein 4
hetero molecules

A: Kv channel-interacting protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2196
Polymers53,0592
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4310 Å2
ΔGint-90 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.300, 96.300, 71.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Kv channel-interacting protein 4 / KChIP4 / A-type potassium channel modulatory protein 4 / Potassium channel-interacting protein 4 / ...KChIP4 / A-type potassium channel modulatory protein 4 / Potassium channel-interacting protein 4 / Calsenilin-like protein


Mass: 26529.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnip4, Calp, Kchip4 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6PHZ8
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CORRECT UNP ACCESSION CODE IS Q6PHZ8-4, IT IS ISOFORM 4.

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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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6-1.8M Ammonium Sulfate, 4%(v/v) iso-Propanol, 0.1M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→99 Å / Num. all: 6677 / Num. obs: 6650 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 37.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 8 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 4.1 / Num. unique all: 668 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KChIP1 (PDB code: 2NZ0)

2nz0


Resolution: 3→20 Å / Isotropic thermal model: MAXIMUM LIKELIHOOD / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2988 6183 -RANDOM
Rwork0.2392 ---
obs0.2392 6545 94.2 %-
all-6567 --
Displacement parametersBiso mean: 52.9479 Å2
Baniso -1Baniso -2Baniso -3
1-16.874 Å20 Å20 Å2
2--16.874 Å20 Å2
3----33.748 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 2 19 1769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.21
LS refinement shellResolution: 3→3.14 Å
RfactorNum. reflection% reflection
Rfree0.466 52 -
Rwork0.406 --
obs-747 100 %

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