[English] 日本語
Yorodumi
- PDB-3eb4: Voltage-dependent K+ channel beta subunit (I211R) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eb4
TitleVoltage-dependent K+ channel beta subunit (I211R) in complex with cortisone
ComponentsVoltage-gated potassium channel subunit beta-2
KeywordsTRANSPORT PROTEIN / oxidoreductase / kvbeta / cortisone / interface / Cytoplasm / Ion transport / Ionic channel / NADP / Phosphoprotein / Potassium / Potassium transport / Transport / Voltage-gated channel
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport ...pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / extrinsic component of cytoplasmic side of plasma membrane / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / neuron projection / axon / glutamatergic synapse / protein-containing complex binding / membrane / cytosol
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, Y. / Weng, J. / Kabaleeswaran, V. / Li, H. / Cao, Y. / Bhosle, R.C. / Zhou, M.
Citation
Journal: Nat.Chem.Biol. / Year: 2008
Title: Cortisone dissociates the Shaker family K+ channels from their beta subunits.
Authors: Pan, Y. / Weng, J. / Kabaleeswaran, V. / Li, H. / Cao, Y. / Bhosle, R.C. / Zhou, M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of a voltage-dependent K+ channel beta subunit.
Authors: Gulbis, J.M. / Mann, S. / MacKinnon, R.
#2: Journal: Science / Year: 2000
Title: Structure of the cytoplasmic beta subunit-T1 assembly of voltage-dependent K+ channels.
Authors: Gulbis, J.M. / Zhou, M. / Mann, S. / MacKinnon, R.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7203
Polymers36,6161
Non-polymers1,1042
Water2,882160
1
A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,88012
Polymers146,4654
Non-polymers4,4158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area15070 Å2
ΔGint-40 kcal/mol
Surface area49280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.260, 113.260, 147.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Voltage-gated potassium channel subunit beta-2 / / K(+) channel subunit beta-2 / Kv-beta-2


Mass: 36616.227 Da / Num. of mol.: 1 / Fragment: cytoplasmic Kvbeta subunit / Mutation: I211R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / References: UniProt: P62483
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PDN / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / PREDNISONE / 1,4 PREGNADIENE-17ALPHA,21-DIOL-3,11,20-TRIONE / 1-CORTISONE / DEHYDROCORTISONE / Prednisone


Mass: 358.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26O5 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6-15% glycerol, 1.5 M ammonium sulfate, 0.1 M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 7.9 - 8.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 26, 2007
RadiationMonochromator: single Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 35198 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.045 / Net I/σ(I): 35.66
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.48 / Num. unique all: 3063 / % possible all: 100

-
Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1EXB, chain A, beta subunit

1exb


Resolution: 2→40.04 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3391309.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1614 5.1 %RANDOM
Rwork0.223 ---
obs0.223 31907 97.6 %-
all-34405 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.3035 Å2 / ksol: 0.35606 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 74 161 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 160 5 %
Rwork0.262 3063 -
obs-3063 56.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2l.paraml.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
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