[English] 日本語
Yorodumi
- PDB-7sit: Crystal structure of Voltage gated potassium ion channel, Kv 1.2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sit
TitleCrystal structure of Voltage gated potassium ion channel, Kv 1.2 chimera-3m
Components
  • Voltage gated potassium channel Kv1.2-Kv2.1
  • Voltage-gated potassium channel subunit beta-2
KeywordsTRANSPORT PROTEIN / OXIDOREDUCTASE / Ion channel / C-type inactivation / Voltage gated Potassium ion channel / Chimera
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 / axon terminus / voltage-gated potassium channel complex / 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 / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXYGEN ATOM / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å
AuthorsReddi, R. / Matulef, K. / Riederer, E.A. / Whorton, M.R. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087546 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for C-type inactivation in a Shaker family voltage-gated K + channel.
Authors: Reddi, R. / Matulef, K. / Riederer, E.A. / Whorton, M.R. / Valiyaveetil, F.I.
History
DepositionOct 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Voltage gated potassium channel Kv1.2-Kv2.1
C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,01311
Polymers192,3534
Non-polymers1,6597
Water0
1
A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,05724
Polymers384,7078
Non-polymers3,35016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area35550 Å2
ΔGint-167 kcal/mol
Surface area110090 Å2
MethodPISA
2
C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,99320
Polymers384,7078
Non-polymers3,28612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area35470 Å2
ΔGint-158 kcal/mol
Surface area109570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.587, 129.587, 278.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-501-

K

21B-502-

K

31B-503-

O

41D-501-

K

51D-502-

K

-
Components

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


Mass: 37353.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Komagataella pastoris (fungus)
References: UniProt: P62483, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein Voltage gated potassium channel Kv1.2-Kv2.1


Mass: 58823.617 Da / Num. of mol.: 2
Mutation: L15H, C31S, C32S, N207Q, W362F, S367T, V377T, C435S, C482S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Komagataella pastoris (fungus)
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris, pH 8.5, 28-32% PEG400, CHAPS / PH range: 8.3-8.8

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.32→49.16 Å / Num. obs: 35720 / % possible obs: 99.9 % / Redundancy: 14.9 % / CC1/2: 0.99 / CC star: 0.54 / Net I/σ(I): 7.2
Reflection shellResolution: 3.32→3.51 Å / Num. unique obs: 4588 / CC1/2: 0.54

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R9R

2r9r


Resolution: 3.32→49.159 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2893 1818 5.09 %
Rwork0.2509 33902 -
obs0.2529 35720 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 299.21 Å2 / Biso mean: 126.359 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.32→49.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10341 0 101 0 10442
Biso mean--62.41 --
Num. residues----1300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3201-3.40980.34471380.36248997
3.4098-3.51010.42391180.3576253198
3.5101-3.62340.39941410.3532255699
3.6234-3.75290.34751420.31122548100
3.7529-3.90310.33421360.2842257599
3.9031-4.08060.27321540.25342560100
4.0806-4.29560.31091370.22232586100
4.2956-4.56460.28261480.20942603100
4.5646-4.91670.22951340.19732614100
4.9167-5.4110.24041230.20142654100
5.411-6.19260.24891460.23352650100
6.1926-7.7970.27221480.25782676100
7.797-49.150.2931530.2544286099

+
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