[English] 日本語
Yorodumi
- PDB-6w85: K2P2.1 (TREK-1):ML335 complex, 200 mM K+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w85
TitleK2P2.1 (TREK-1):ML335 complex, 200 mM K+
ComponentsPotassium channel subfamily K member 2
KeywordsMETAL TRANSPORT / ion channel / K2P / TREK1 / TREK-1
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity / negative regulation of DNA biosynthetic process / cochlea development / voltage-gated potassium channel activity / calyx of Held / response to axon injury / voltage-gated potassium channel complex / axon terminus / response to mechanical stimulus / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / memory / cellular response to hypoxia / apical plasma membrane / G protein-coupled receptor signaling pathway / axon / neuronal cell body / cell surface / endoplasmic reticulum / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
: / DECANE / : / N-OCTANE / Chem-Q6F / HEXADECANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLolicato, M. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NIH-R01-MH093603 United States
CitationJournal: Sci Adv / Year: 2020
Title: K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions.
Authors: Lolicato, M. / Natale, A.M. / Abderemane-Ali, F. / Crottes, D. / Capponi, S. / Duman, R. / Wagner, A. / Rosenberg, J.M. / Grabe, M. / Minor Jr., D.L.
History
DepositionMar 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Potassium channel subfamily K member 2
B: Potassium channel subfamily K member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,76918
Polymers68,6082
Non-polymers2,16116
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-96 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.177, 120.65, 129.795
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel subfamily K member 2 / Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore ...Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore potassium channel TPKC1


Mass: 34303.938 Da / Num. of mol.: 2
Mutation: K84R, Q85E, T86K, I88L, A89R, Q90A, A92P, N95S, S96D, T97Q, N119A, S300A, E306A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnk2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438

-
Non-polymers , 6 types, 16 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-Q6F / N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide


Mass: 373.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14Cl2N2O3S
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#7: Chemical ChemComp-R16 / HEXADECANE / Hexadecane


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22-25% PEG400, 100mM HEPES pH=8.0, 1mM CdCl2, 200mM KCl

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
2451N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONDiamond I2322.75
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 1, 2019
DECTRIS PILATUS 12M2PIXELMar 4, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2silicon crystal
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
22.751
ReflectionResolution: 3.8→47.65 Å / Num. obs: 11399 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.6
Reflection shellResolution: 3.8→4.25 Å / Num. unique obs: 3165 / CC1/2: 0.113

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
GDA2.11.4data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cq6

6cq6


Resolution: 3.8→14.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.687
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 519 -RANDOM
Rwork0.2419 ---
obs0.2443 11143 99.9 %-
Displacement parametersBiso mean: 234.69 Å2
Baniso -1Baniso -2Baniso -3
1--15.7505 Å20 Å20 Å2
2--17.8236 Å20 Å2
3----2.0731 Å2
Refine analyzeLuzzati coordinate error obs: 0.79 Å
Refinement stepCycle: LAST / Resolution: 3.8→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 117 0 4459
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114562HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.16181HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1519SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes731HARMONIC5
X-RAY DIFFRACTIONt_it4458HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion616SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3652SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.98
X-RAY DIFFRACTIONt_other_torsion17.31
LS refinement shellResolution: 3.8→3.85 Å
RfactorNum. reflection% reflection
Rfree0.2778 20 -
Rwork0.2802 --
obs0.2801 446 98.68 %
Refinement TLS params.

S22: 0.0042 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50620.1343-0.2250.13520.27360.68370.0004-0.0087-0.0049-0.00870.0083-0.00490.0083-0.0046-0.0028-0.00280.0047-0.0019-0.01060.00181.1692-20.55921.4389
20.22550.3855-0.03850.5592-0.27970.504-0.0001-0.00430.0072-0.0043-0.00290.0072-0.0029-0.00410.0012-0.0008-0.0038-0.0031-0.00650.0037-4.8726-27.380833.6603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - A|321 A|401 - A|403 }A35 - 321
2X-RAY DIFFRACTION1{ A|35 - A|321 A|401 - A|403 }A401 - 403
3X-RAY DIFFRACTION2{ A|404 - A|405 B|35 - B|316 B|401 - B|404 }A404 - 405
4X-RAY DIFFRACTION2{ A|404 - A|405 B|35 - B|316 B|401 - B|404 }B35 - 316
5X-RAY DIFFRACTION2{ A|404 - A|405 B|35 - B|316 B|401 - B|404 }B401 - 404

+
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