[English] 日本語
Yorodumi
- PDB-6fbk: Crystal structure of the human WNK2 CCT-like 1 domain in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fbk
TitleCrystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide
Components
  • Serine/threonine-protein kinase WNK1
  • Serine/threonine-protein kinase WNK2
KeywordsPEPTIDE BINDING PROTEIN / WNK2 / CCT Domain / AI domain / RFXV motif binding
Function / homology
Function and homology information


positive regulation of sodium ion transmembrane transporter activity / negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / monoatomic cation homeostasis / positive regulation of termination of RNA polymerase II transcription / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / negative regulation of small GTPase mediated signal transduction / monoatomic ion homeostasis ...positive regulation of sodium ion transmembrane transporter activity / negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / monoatomic cation homeostasis / positive regulation of termination of RNA polymerase II transcription / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / negative regulation of small GTPase mediated signal transduction / monoatomic ion homeostasis / negative regulation of sodium ion transport / positive regulation of mitotic cytokinesis / regulation of mRNA export from nucleus / negative regulation of heterotypic cell-cell adhesion / intracellular chloride ion homeostasis / positive regulation of T cell chemotaxis / regulation of sodium ion transmembrane transport / cellular response to chemokine / potassium ion homeostasis / negative regulation of leukocyte cell-cell adhesion / membraneless organelle assembly / cellular hyperosmotic response / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / intracellular membraneless organelle / positive regulation of systemic arterial blood pressure / protein kinase activator activity / negative regulation of protein localization to plasma membrane / neuron development / phosphatase binding / regulation of sodium ion transport / monoatomic ion transport / negative regulation of protein ubiquitination / sodium ion transmembrane transport / negative regulation of autophagy / molecular condensate scaffold activity / negative regulation of ERK1 and ERK2 cascade / Stimuli-sensing channels / positive regulation of angiogenesis / mitotic spindle / positive regulation of canonical Wnt signaling pathway / T cell receptor signaling pathway / heart development / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein kinase binding / signal transduction / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / WNK CCTL2 domain / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...: / : / WNK CCTL2 domain / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase WNK1 / Serine/threonine-protein kinase WNK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Crystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide
Authors: Pinkas, D.M. / Bufton, J.C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Serine/threonine-protein kinase WNK2
P: Serine/threonine-protein kinase WNK1


Theoretical massNumber of molelcules
Total (without water)13,9512
Polymers13,9512
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.047, 78.047, 37.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Serine/threonine-protein kinase WNK2 / Antigen NY-CO-43 / Protein kinase lysine-deficient 2 / Protein kinase with no lysine 2 / ...Antigen NY-CO-43 / Protein kinase lysine-deficient 2 / Protein kinase with no lysine 2 / Serologically defined colon cancer antigen 43


Mass: 11340.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK2, KIAA1760, PRKWNK2, SDCCAG43, P/OKcl.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q9Y3S1, non-specific serine/threonine protein kinase
#2: Protein/peptide Serine/threonine-protein kinase WNK1 / Erythrocyte 65 kDa protein / p65 / Kinase deficient protein / Protein kinase lysine-deficient 1 / ...Erythrocyte 65 kDa protein / p65 / Kinase deficient protein / Protein kinase lysine-deficient 1 / Protein kinase with no lysine 1 / hWNK1


Mass: 2610.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9H4A3, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium fluoride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→55.3 Å / Num. obs: 11689 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 20.7
Reflection shellResolution: 1.743→1.773 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ELM

6elm


Resolution: 1.743→33.973 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 50.6
Details: Refinement R factors are higher than expected for resolution and diffraction images show diffuse spots between the indexed spots that were not able to be integrated. Nevertheless, the structure appears correct.
RfactorNum. reflection% reflection
Rfree0.3341 551 4.72 %
Rwork0.2844 --
obs0.2869 11674 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.743→33.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 0 14 774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008771
X-RAY DIFFRACTIONf_angle_d0.8741045
X-RAY DIFFRACTIONf_dihedral_angle_d23.092460
X-RAY DIFFRACTIONf_chiral_restr0.054124
X-RAY DIFFRACTIONf_plane_restr0.006135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7429-1.91830.44661450.46192778X-RAY DIFFRACTION100
1.9183-2.19580.45511220.3912706X-RAY DIFFRACTION97
2.1958-2.76630.44411470.37652772X-RAY DIFFRACTION100
2.7663-33.97970.29011370.2392867X-RAY DIFFRACTION100

+
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