[English] 日本語
Yorodumi
- PDB-1s6c: Crystal structure of the complex between KChIP1 and Kv4.2 N1-30 -

+
Open data


ID or keywords:

Loading...

-
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 / Kv4.3-KChIP1 channel complex / Kv4.2-KChIP2 channel complex / cardiac muscle cell action potential / A-type (transient outward) potassium channel activity / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / perinuclear endoplasmic reticulum / positive regulation of action potential ...Phase 1 - inactivation of fast Na+ channels / Kv4.3-KChIP1 channel complex / Kv4.2-KChIP2 channel complex / cardiac muscle cell action potential / A-type (transient outward) potassium channel activity / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / perinuclear endoplasmic reticulum / positive regulation of action potential / membrane repolarization / regulation of potassium ion transmembrane transport / anchoring junction / postsynaptic specialization membrane / neuronal cell body membrane / locomotor rhythm / monoatomic ion channel activity / action potential / plasma membrane raft / voltage-gated potassium channel activity / regulation of signal transduction / potassium channel activity / potassium channel regulator activity / neuronal action potential / voltage-gated potassium channel complex / potassium ion transmembrane transport / sensory perception of pain / T-tubule / muscle contraction / cellular response to mechanical stimulus / protein homooligomerization / sarcolemma / GABA-ergic synapse / caveola / potassium ion transport / cytoplasmic side of plasma membrane / cellular response to xenobiotic stimulus / perikaryon / cellular response to hypoxia / dendritic spine / transmembrane transporter binding / postsynaptic membrane / neuronal cell body / calcium ion binding / dendrite / protein-containing complex binding / glutamatergic synapse / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.2 / 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, Kv4.2 / 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 / Voltage-gated potassium channel / 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
A-type voltage-gated potassium channel KCND2 / A-type potassium channel modulatory protein KCNIP1
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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more