[English] 日本語
Yorodumi
- PDB-8ctx: Crystal structure of a K+ selective NaK mutant (NaK2K) -K+,Tl+ complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ctx
TitleCrystal structure of a K+ selective NaK mutant (NaK2K) -K+,Tl+ complex
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Potassium ion channel / thallium ion / Tl+
Function / homology
Function and homology information


potassium channel activity / membrane
Similarity search - Function
Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / THALLIUM (I) ION / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus m1550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM12345 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM141697 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM118217 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)DP2OD028805 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Kinship FoundationSSP-2018-3240 United States
New York Community Trust338034 United States
CitationJournal: To Be Published
Title: Direct visualization of electric field-stimulated ion conduction in a potassium channel
Authors: Lee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,60715
Polymers21,2812
Non-polymers2,32613
Water19811
1
A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78036
Polymers42,5624
Non-polymers5,21832
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 area10720 Å2
ΔGint-176 kcal/mol
Surface area16190 Å2
MethodPISA
2
B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,65024
Polymers42,5624
Non-polymers4,08820
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 area8630 Å2
ΔGint-129 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.461, 68.461, 90.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

TL

21A-202-

TL

31A-203-

TL

41A-204-

TL

51A-207-

K

61A-208-

K

71B-201-

TL

81B-202-

TL

91B-203-

TL

101B-204-

TL

-
Components

#1: Protein Potassium channel protein


Mass: 10640.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus m1550 (bacteria) / Gene: bcere0011_5790 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: C2R3K4
#2: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Tl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NaK2K protein was mixed with 50mM MES pH 6.5/100mM potassium citrate/200mM TlNO3/56%-68% MPD while 50mM MES pH 6.5/100mM potassium citrate/200mM KNO3/56%-68% MPD was used for the reservoir

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97864 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 27873 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 43.32 Å2 / Rsym value: 0.132 / Net I/σ(I): 20.292
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.821 / Num. unique obs: 1375 / CC1/2: 0.598 / Rsym value: 1.327 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OUF

3ouf


Resolution: 1.99→34.23 Å / SU ML: 0.2491 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 33.1898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2541 2783 9.99 %
Rwork0.2143 25067 -
obs0.2181 27850 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.52 Å2
Refinement stepCycle: LAST / Resolution: 1.99→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 13 11 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711760
X-RAY DIFFRACTIONf_angle_d0.84422422
X-RAY DIFFRACTIONf_chiral_restr0.0478303
X-RAY DIFFRACTIONf_plane_restr0.006301
X-RAY DIFFRACTIONf_dihedral_angle_d12.9121603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.38111330.31611212X-RAY DIFFRACTION95.53
2.03-2.060.35071250.28681298X-RAY DIFFRACTION99.51
2.06-2.10.30471500.26671199X-RAY DIFFRACTION99.93
2.1-2.150.30421500.24761275X-RAY DIFFRACTION99.65
2.15-2.190.30731430.241200X-RAY DIFFRACTION96.9
2.19-2.240.25311400.22851241X-RAY DIFFRACTION100
2.25-2.30.27881350.20161306X-RAY DIFFRACTION100
2.3-2.360.27941420.20261253X-RAY DIFFRACTION100
2.36-2.430.27051430.21711246X-RAY DIFFRACTION100
2.43-2.510.28881240.18671268X-RAY DIFFRACTION99.93
2.51-2.60.2211370.161241X-RAY DIFFRACTION99.78
2.6-2.710.21771520.17191233X-RAY DIFFRACTION99.93
2.71-2.830.25141290.2161279X-RAY DIFFRACTION98.32
2.83-2.980.24571280.23541264X-RAY DIFFRACTION99.57
2.98-3.160.26461490.22691267X-RAY DIFFRACTION100
3.16-3.410.23961320.21191245X-RAY DIFFRACTION100
3.41-3.750.24621420.24081257X-RAY DIFFRACTION99.86
3.75-4.290.21751360.20181256X-RAY DIFFRACTION99.5
4.3-5.390.24911440.18981271X-RAY DIFFRACTION99.93
5.41-34.230.26431490.22541256X-RAY DIFFRACTION99.43

+
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