[English] 日本語
Yorodumi
- PDB-6u9p: Wild-type MthK pore in ~150 mM K+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u9p
TitleWild-type MthK pore in ~150 mM K+
ComponentsCalcium-gated potassium channel MthK
KeywordsTRANSPORT PROTEIN / Potassium ion channel MthK
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / Potassium channel domain / Ion channel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / : / Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPosson, D.J. / Nimigean, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088352 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM087865 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Selectivity filter ion binding affinity determines inactivation in a potassium channel.
Authors: Boiteux, C. / Posson, D.J. / Allen, T.W. / Nimigean, C.M.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2937
Polymers8,9801
Non-polymers3146
Water54030
1
A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17328
Polymers35,9184
Non-polymers1,25524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area6520 Å2
ΔGint-63 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.811, 63.811, 44.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51A-105-

K

-
Components

#1: Protein Calcium-gated potassium channel MthK


Mass: 8979.500 Da / Num. of mol.: 1 / Fragment: UNP residues 18-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1:1 protein (in 100 mM potassium chloride, 10 mM MOPS-KOH, pH 8.0) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-KOH, pH 6.75

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→44.05 Å / Num. obs: 11414 / % possible obs: 99.87 % / Redundancy: 23.2 % / Biso Wilson estimate: 22.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1037 / Rpim(I) all: 0.02178 / Rrim(I) all: 0.1061 / Net I/σ(I): 19.15
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.67 / Num. unique obs: 1096 / CC1/2: 0.653 / Rpim(I) all: 0.4666 / Rrim(I) all: 1.735 / % possible all: 98.92

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LDC

3ldc


Resolution: 1.65→44.05 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8366
RfactorNum. reflection% reflection
Rfree0.2075 1141 10.05 %
Rwork0.1829 --
obs0.1852 11408 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.89 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 13 30 680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192687
X-RAY DIFFRACTIONf_angle_d1.2721946
X-RAY DIFFRACTIONf_chiral_restr0.1039119
X-RAY DIFFRACTIONf_plane_restr0.0114111
X-RAY DIFFRACTIONf_dihedral_angle_d2.6884501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.32721460.29071096X-RAY DIFFRACTION98.92
1.69-1.730.29041420.2771264X-RAY DIFFRACTION100
1.73-1.780.25821220.22791255X-RAY DIFFRACTION100
1.78-1.830.24321500.22411245X-RAY DIFFRACTION99.86
1.83-1.890.19721320.19781256X-RAY DIFFRACTION100
1.89-1.960.20441450.17781230X-RAY DIFFRACTION100
1.96-2.040.22431400.18461267X-RAY DIFFRACTION100
2.04-2.130.161500.17191249X-RAY DIFFRACTION100
2.13-2.240.23121490.16211229X-RAY DIFFRACTION100
2.24-2.380.17251680.16671229X-RAY DIFFRACTION100
2.38-2.560.18531360.1521268X-RAY DIFFRACTION100
2.56-2.820.20051290.15261260X-RAY DIFFRACTION100
2.82-3.230.16951170.16121288X-RAY DIFFRACTION100
3.23-4.070.20181420.18181245X-RAY DIFFRACTION100
4.07-44.050.23191290.20321274X-RAY DIFFRACTION99.93
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)
14.348079721451.520920671713.724831868764.542872775860.8705190055045.007526827320.0105343693152-0.57925259812-0.06646372496620.3626857804750.1119297798260.0871711278930.00766738861063-0.429995423673-0.09313498339150.2209603293280.08389718372280.006441054055980.2676245527680.009279558010510.2043302468167.6877023788414.77015742384.42575340469
22.00013572497-0.6033512703290.4086847420953.33070879725-0.01251288175533.052900664950.1464808902320.224754747718-0.158376135567-0.196508222521-0.0488227241515-0.06105623135830.4608089147860.108847409968-0.1064997014830.2405375426770.021885455513-0.02475006902630.192696967356-0.01559248017590.1827085536153.5416246993318.9358286142-12.7218867577
38.869815035461.016683733096.181685752032.15797246951.765773712127.72396658192-0.0468040709504-0.308203354072-0.3014718250050.08578267519750.1144329532910.09791061196670.0939298395978-0.223330911863-0.05447262961280.236353998743-0.00649760471392-0.001071081401820.1655858914750.04841106009530.179925131632-1.1792874576419.2567870297-1.61184490872
44.825844189532.98349546244-2.364786444423.770414433581.214943090044.879754212160.112496056624-1.520886983850.4467239110631.47173905694-0.174912228557-0.7890857312070.2189980697881.662786711560.06117909979090.897914453561-0.0305995764868-0.3530845697860.665501326087-0.05630483771220.62961884151912.852751995626.916060885510.0080264934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:34)
2X-RAY DIFFRACTION2(chain A and resid 35:73)
3X-RAY DIFFRACTION3(chain A and resid 74:90)
4X-RAY DIFFRACTION4(chain A and resid 91:99)

+
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