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- PDB-1s1e: Crystal Structure of Kv Channel-interacting protein 1 (KChIP-1) -

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Basic information

Entry
Database: PDB / ID: 1s1e
TitleCrystal Structure of Kv Channel-interacting protein 1 (KChIP-1)
ComponentsKv channel interacting protein 1
KeywordsTRANSPORT PROTEIN / KChIP / Kv Channel-interacting protein / Calcium-binding protein / EF-finger
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 / cytoplasmic side of plasma membrane / transmembrane transporter binding / calcium ion binding / dendrite / plasma membrane / cytoplasm
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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. / ...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 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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.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_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

Downloads & links

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Assembly

Deposited unit
A: Kv channel interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4253
Polymers26,3451
Non-polymers802
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.133, 50.133, 177.329
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 Kv channel interacting protein 1


Mass: 26344.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNIP1 / Plasmid: pET-21b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZI2
#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.: 123 / 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: 2.66 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG3350,Calcium chloride, Ammonium Chloride, DTT, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 143 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.45 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 10898 / Num. obs: 10497 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rsym value: 0.066 / Net I/σ(I): 25.6
Reflection shellResolution: 2.3→2.38 Å / % possible all: 95

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJF

1bjf


Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2732 465 RANDOM
Rwork0.2238 --
all0.252 10684 -
obs0.25 8417 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 2 123 1619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.117

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