[English] 日本語
Yorodumi
- PDB-6rv2: Crystal structure of the human two pore domain potassium ion chan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rv2
TitleCrystal structure of the human two pore domain potassium ion channel TASK-1 (K2P3.1) in a closed conformation
ComponentsPotassium channel subfamily K member 3
KeywordsMEMBRANE PROTEIN / potassium channel / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


open rectifier potassium channel activity / detection of hypoxic conditions in blood by carotid body chemoreceptor signaling / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / S100 protein binding ...open rectifier potassium channel activity / detection of hypoxic conditions in blood by carotid body chemoreceptor signaling / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / S100 protein binding / negative regulation of cytosolic calcium ion concentration / cellular response to zinc ion / sodium channel activity / monoatomic ion channel activity / cochlea development / potassium channel activity / potassium ion transmembrane transport / potassium ion transport / monoatomic ion transmembrane transport / cellular response to hypoxia / chemical synaptic transmission / response to xenobiotic stimulus / protein heterodimerization activity / synapse / metal ion binding / plasma membrane
Similarity search - Function
Potassium channel subfamily K member 3 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / CHOLESTEROL HEMISUCCINATE / Potassium channel subfamily K member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRodstrom, K.E.J. / Pike, A.C.W. / Zhang, W. / Quigley, A. / Speedman, D. / Mukhopadhyay, S.M.M. / Shrestha, L. / Chalk, R. / Venkaya, S. / Bushell, S.R. ...Rodstrom, K.E.J. / Pike, A.C.W. / Zhang, W. / Quigley, A. / Speedman, D. / Mukhopadhyay, S.M.M. / Shrestha, L. / Chalk, R. / Venkaya, S. / Bushell, S.R. / Tessitore, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N009274/1 United Kingdom
CitationJournal: Nature / Year: 2020
Title: A lower X-gate in TASK channels traps inhibitors within the vestibule.
Authors: Rodstrom, K.E.J. / Kiper, A.K. / Zhang, W. / Rinne, S. / Pike, A.C.W. / Goldstein, M. / Conrad, L.J. / Delbeck, M. / Hahn, M.G. / Meier, H. / Platzk, M. / Quigley, A. / Speedman, D. / ...Authors: Rodstrom, K.E.J. / Kiper, A.K. / Zhang, W. / Rinne, S. / Pike, A.C.W. / Goldstein, M. / Conrad, L.J. / Delbeck, M. / Hahn, M.G. / Meier, H. / Platzk, M. / Quigley, A. / Speedman, D. / Shrestha, L. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / Tucker, S.J. / Muller, T. / Decher, N. / Carpenter, E.P.
History
DepositionMay 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium channel subfamily K member 3
B: Potassium channel subfamily K member 3
C: Potassium channel subfamily K member 3
D: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,79626
Polymers120,4684
Non-polymers8,32822
Water55831
1
A: Potassium channel subfamily K member 3
B: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,88314
Polymers60,2342
Non-polymers4,64912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-122 kcal/mol
Surface area24430 Å2
MethodPISA
2
C: Potassium channel subfamily K member 3
D: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,91312
Polymers60,2342
Non-polymers3,67910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-124 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.140, 204.790, 238.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

-
Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein
Potassium channel subfamily K member 3 / Acid-sensitive potassium channel protein TASK-1 / TWIK-related acid-sensitive K(+) channel 1 / Two ...Acid-sensitive potassium channel protein TASK-1 / TWIK-related acid-sensitive K(+) channel 1 / Two pore potassium channel KT3.1 / Two pore K(+) channel KT3.1


Mass: 30117.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK3, TASK, TASK1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14649
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 50 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C31H50O4
#5: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS pH 8.5, 0.05 M KCl, 32% v/v PEG400, 3% w/v sucrose
Temp details: Ambient

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3→47.668 Å / Num. obs: 36417 / % possible obs: 79.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 75.54 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.103 / Rrim(I) all: 0.239 / Net I/σ(I): 5.6
Reflection shellResolution: 3→3.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1822 / CC1/2: 0.697 / Rpim(I) all: 0.464 / Rrim(I) all: 1.124 / % possible all: 37.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018data reduction
XSCALEVERSION Mar 15, 2019data scaling
STARANISO2.2.19data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW5

4bw5


Resolution: 3→47.04 Å / Cor.coef. Fo:Fc: 0.808 / Cor.coef. Fo:Fc free: 0.841 / SU R Cruickshank DPI: 1.499 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.417 / SU Rfree Blow DPI: 0.392 / SU Rfree Cruickshank DPI: 0.4
Details: Refined against STARANISO anisotropically truncated data
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1756 4.83 %RANDOM
Rwork0.253 ---
obs0.254 36373 79.7 %-
Displacement parametersBiso mean: 66.77 Å2
Baniso -1Baniso -2Baniso -3
1--13.8238 Å20 Å20 Å2
2--10.7283 Å20 Å2
3---3.0955 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 426 31 8466
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088623HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.911696HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3090SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1405HARMONIC5
X-RAY DIFFRACTIONt_it8623HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.03
X-RAY DIFFRACTIONt_other_torsion17.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance64HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10204SEMIHARMONIC4
LS refinement shellResolution: 3→3.05 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2558 -5.36 %
Rwork0.2288 689 -
all0.2303 728 -
obs--35.86 %
Refinement TLS params.

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 °)S22 (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)
12.6606-0.49430.31031.6699-0.36952.19260.06010.0939-0.2428-0.1763-0.1832-0.11380.07860.1330.1231-0.39930.00510.01380.01250.1461-0.18572.8402-40.853525.7508
22.41650.05830.18291.1463-0.43291.37380.0148-0.01320.0371-0.0417-0.0520.2460.0482-0.20380.0372-0.3471-0.0089-0.00390.01290.1504-0.0825-8.4415-37.274429.3343
32.93760.13760.232.23-0.71732.1015-0.0490.05340.2297-0.1019-0.04820.075-0.0606-0.1080.0972-0.45370.02730.02940.03940.0184-0.1763-25.290122.81833.041
43.08780.1747-0.0611.6474-0.58852.273-0.0013-0.1963-0.02720.00710.1433-0.0460.03720.0922-0.142-0.41730.00840.0362-0.01310.0947-0.106-13.629719.102336.7996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 304}
2X-RAY DIFFRACTION2{B|1 - 261}
3X-RAY DIFFRACTION3{C|1 - 304}
4X-RAY DIFFRACTION4{D|1 - 261}

+
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