[English] 日本語
Yorodumi
- PDB-6ufe: The structure of a potassium selective ion channel at atomic reso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ufe
TitleThe structure of a potassium selective ion channel at atomic resolution
ComponentsTransporter
KeywordsMEMBRANE PROTEIN / ion channel / potassium ion channel
Function / homology
Function and homology information


potassium channel activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
: / Transporter / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLangan, P.S. / Vandavasi, V.G. / Sullivan, B. / Afonine, P.V. / Weiss, K.L.
CitationJournal: Iucrj / Year: 2020
Title: The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation.
Authors: Langan, P.S. / Vandavasi, V.G. / Kopec, W. / Sullivan, B. / Afonne, P.V. / Weiss, K.L. / de Groot, B.L. / Coates, L.
History
DepositionSep 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,88620
Polymers20,3922
Non-polymers1,49518
Water1,49583
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules

A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,30036
Polymers40,7844
Non-polymers2,51632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area10670 Å2
ΔGint-197 kcal/mol
Surface area16160 Å2
MethodPISA
2
B: Transporter
hetero molecules

B: Transporter
hetero molecules

B: Transporter
hetero molecules

B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,24644
Polymers40,7844
Non-polymers3,46240
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area14370 Å2
ΔGint-309 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 67.860, 89.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-705-

K

21A-706-

K

31A-707-

K

41A-708-

K

51B-203-

K

61B-204-

K

71B-205-

K

81B-206-

K

-
Components

#1: Protein Transporter / Voltage-gated potassium channel


Mass: 10195.952 Da / Num. of mol.: 2 / Mutation: D66Y, N68D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: A9485_19160, BACERE00184_02078, CJ306_03585, CN950_06075, CN980_22870, COI98_17615, CON37_12595
Production host: Escherichia coli (E. coli) / References: UniProt: A0A164U772, UniProt: Q81HW2*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: See paper for details

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 61537 / % possible obs: 97.4 % / Redundancy: 5.34 % / CC1/2: 0.998 / Net I/σ(I): 12.23
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 3673 / CC1/2: 0.489

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OUF

3ouf


Resolution: 1.2→21.459 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1477 2013 3.27 %
Rwork0.1326 --
obs0.1331 61528 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→21.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 88 83 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.031673
X-RAY DIFFRACTIONf_angle_d4.092324
X-RAY DIFFRACTIONf_dihedral_angle_d157.09592
X-RAY DIFFRACTIONf_chiral_restr0.36290
X-RAY DIFFRACTIONf_plane_restr0.03269
LS refinement shellResolution: 1.2→1.23 Å
RfactorNum. reflection% reflection
Rfree0.2925 124 -
Rwork0.2876 3393 -
obs--78 %

+
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