[English] 日本語
Yorodumi
- PDB-6v3i: K2P2.1(TREK-1)I110D:RuR bound channel structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v3i
TitleK2P2.1(TREK-1)I110D:RuR bound channel structure
ComponentsPotassium channel subfamily K member 2
KeywordsMEMBRANE PROTEIN / K channel / TREK-1 / Mus musculus
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / cellular response to arachidonate / mechanosensitive potassium channel activity / positive regulation of cellular response to hypoxia / stabilization of membrane potential / detection of mechanical stimulus involved in sensory perception of touch / chemical synaptic transmission, postsynaptic / cardiac ventricle development / ligand-gated channel activity ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / cellular response to arachidonate / mechanosensitive potassium channel activity / positive regulation of cellular response to hypoxia / stabilization of membrane potential / detection of mechanical stimulus involved in sensory perception of touch / chemical synaptic transmission, postsynaptic / cardiac ventricle development / ligand-gated channel activity / negative regulation of cardiac muscle cell proliferation / potassium ion leak channel activity / negative regulation of DNA biosynthetic process / astrocyte projection / node of Ranvier / outward rectifier potassium channel activity / glutamate secretion / cochlea development / regulation of synaptic transmission, GABAergic / voltage-gated potassium channel activity / response to axon injury / neuronal action potential / voltage-gated potassium channel complex / calyx of Held / chloride transmembrane transport / regulation of membrane potential / postsynaptic density membrane / potassium ion transport / sarcolemma / Schaffer collateral - CA1 synapse / memory / cellular response to hypoxia / G protein-coupled receptor signaling pathway / apical plasma membrane / protein heterodimerization activity / neuronal cell body / dendrite / cell surface / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DODECANE / HEXANE / : / PENTANE / N-OCTANE / Chem-R2R / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPope, L. / Lolicato, M. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)NIH-R01-MH093603 United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: Polynuclear Ruthenium Amines Inhibit K2PChannels via a "Finger in the Dam" Mechanism.
Authors: Pope, L. / Lolicato, M. / Minor Jr., D.L.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

-
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)70,71619
Polymers68,6122
Non-polymers2,10417
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-84 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.945, 120.303, 127.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 46 through 75 or (resid 76...
21(chain B and (resid 46 through 83 or resid 86...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 46 through 75 or (resid 76...A46 - 75
121(chain A and (resid 46 through 75 or (resid 76...A76
131(chain A and (resid 46 through 75 or (resid 76...A45 - 320
141(chain A and (resid 46 through 75 or (resid 76...A45 - 320
151(chain A and (resid 46 through 75 or (resid 76...A45 - 320
161(chain A and (resid 46 through 75 or (resid 76...A45 - 320
211(chain B and (resid 46 through 83 or resid 86...B46 - 83
221(chain B and (resid 46 through 83 or resid 86...B86 - 90
231(chain B and (resid 46 through 83 or resid 86...B92 - 93
241(chain B and (resid 46 through 83 or resid 86...B95 - 96
251(chain B and (resid 46 through 83 or resid 86...B37 - 316
261(chain B and (resid 46 through 83 or resid 86...B37 - 316
271(chain B and (resid 46 through 83 or resid 86...B37 - 316
281(chain B and (resid 46 through 83 or resid 86...B37 - 316
291(chain B and (resid 46 through 83 or resid 86...B233 - 253
2101(chain B and (resid 46 through 83 or resid 86...B268
2111(chain B and (resid 46 through 83 or resid 86...B270
2121(chain B and (resid 46 through 83 or resid 86...B0
2131(chain B and (resid 46 through 83 or resid 86...B37 - 316
2141(chain B and (resid 46 through 83 or resid 86...B37 - 316
2151(chain B and (resid 46 through 83 or resid 86...B312 - 31

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel subfamily K member 2


Mass: 34305.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438*PLUS

-
Non-polymers , 8 types, 19 molecules

#2: Chemical ChemComp-R2R / ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)


Mass: 559.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H28N14O2Ru3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#8: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M KCl, 1-3 mM CdCl2, 0.1 M HEPES pH 7-8, 20-26% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.39→46.6 Å / Num. obs: 15118 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
3.4-3.676.730530.1281100
9-46.745.69050.999198.8

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RUE

4rue


Resolution: 3.4→15 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.46
RfactorNum. reflection% reflection
Rfree0.3278 653 4.57 %
Rwork0.2755 --
obs0.2778 14286 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 723.68 Å2 / Biso mean: 193.6429 Å2 / Biso min: 122.23 Å2
Refinement stepCycle: final / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 135 2 4207
Biso mean--206.24 125.85 -
Num. residues----526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1732X-RAY DIFFRACTIONPOSITIONAL1.391
12B1732X-RAY DIFFRACTIONPOSITIONAL1.391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.39-3.650.47481050.46382219232479
3.65-4.010.3991370.372928162953100
4.01-4.580.33191120.289428232935100
4.58-5.710.29981560.287128372993100
5.71-150.32121430.244729383081100

+
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