[English] 日本語
Yorodumi
- PDB-3pjs: Mechanism of Activation Gating in the Full-Length KcsA K+ Channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pjs
TitleMechanism of Activation Gating in the Full-Length KcsA K+ Channel
Components
  • FAB heavy chainFragment antigen-binding
  • FAB light chainFragment antigen-binding
  • Voltage-gated potassium channel
KeywordsTRANSPORT PROTEIN / Ion channel / conducts K+ ions / Cell membrane
Function / homology
Function and homology information


monoatomic ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich ...ATP synthase delta/epsilon subunit, C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsUysal, S. / Cuello, L.G. / Kossiakoff, A. / Perozo, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Mechanism of activation gating in the full-length KcsA K+ channel.
Authors: Uysal, S. / Cuello, L.G. / Cortes, D.M. / Koide, S. / Kossiakoff, A.A. / Perozo, E.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Aug 3, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FAB light chain
B: FAB heavy chain
C: FAB light chain
D: FAB heavy chain
K: Voltage-gated potassium channel
L: Voltage-gated potassium channel
M: Voltage-gated potassium channel
N: Voltage-gated potassium channel


Theoretical massNumber of molelcules
Total (without water)168,9738
Polymers168,9738
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.266, 176.716, 340.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Antibody FAB light chain / Fragment antigen-binding


Mass: 23562.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody FAB heavy chain / Fragment antigen-binding


Mass: 23905.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein
Voltage-gated potassium channel / / KcsA


Mass: 18509.361 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.71 Å3/Da / Density % sol: 78.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Na/K phosphate, 0.1M Bis-Tris propane pH 7.5, 10% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 35572 / Num. obs: 29324 / % possible obs: 82.4 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6
Reflection shellHighest resolution: 3.8 Å / % possible all: 93.9

-
Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3322 1358 3.8 %RANDOM
Rwork0.2814 27966 --
all-35414 --
obs-29324 82.4 %-
Solvent computationBsol: 124.786 Å2
Displacement parametersBiso max: 222.19 Å2 / Biso mean: 177.8122 Å2 / Biso min: 30.56 Å2
Baniso -1Baniso -2Baniso -3
1--15.729 Å20 Å20 Å2
2---6.642 Å20 Å2
3---22.371 Å2
Refinement stepCycle: LAST / Resolution: 3.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10982 0 0 0 10982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d2.29
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

+
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