[English] 日本語
Yorodumi
- PDB-6gzd: Crystal structure of Human CSNK1A1 with A86 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gzd
TitleCrystal structure of Human CSNK1A1 with A86
ComponentsCasein kinase I isoform alpha
KeywordsTRANSFERASE / CKIa / Casein kinase / Kinase inhibitor
Function / homology
Function and homology information


Activation of SMO / intermediate filament cytoskeleton organization / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants ...Activation of SMO / intermediate filament cytoskeleton organization / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / positive regulation of Rho protein signal transduction / Golgi organization / positive regulation of TORC1 signaling / ciliary basal body / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / cilium / Wnt signaling pathway / kinetochore / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / viral protein processing / protein kinase activity / nuclear speck / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LCI / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3,3',3''-phosphanetriyltripropanoic acid / Casein kinase I isoform alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBen-Neriah, Y. / Venkatachalam, A. / Minzel, W. / Fink, A. / Snir-Alkalay, I. / Vacca, J.
CitationJournal: Cell / Year: 2018
Title: Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models.
Authors: Minzel, W. / Venkatachalam, A. / Fink, A. / Hung, E. / Brachya, G. / Burstain, I. / Shaham, M. / Rivlin, A. / Omer, I. / Zinger, A. / Elias, S. / Winter, E. / Erdman, P.E. / Sullivan, R.W. / ...Authors: Minzel, W. / Venkatachalam, A. / Fink, A. / Hung, E. / Brachya, G. / Burstain, I. / Shaham, M. / Rivlin, A. / Omer, I. / Zinger, A. / Elias, S. / Winter, E. / Erdman, P.E. / Sullivan, R.W. / Fung, L. / Mercurio, F. / Li, D. / Vacca, J. / Kaushansky, N. / Shlush, L. / Oren, M. / Levine, R. / Pikarsky, E. / Snir-Alkalay, I. / Ben-Neriah, Y.
History
DepositionJul 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
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_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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: Casein kinase I isoform alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,22519
Polymers43,0751
Non-polymers2,14918
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-15 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.383, 113.383, 80.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Casein kinase I isoform alpha / CKI-alpha / CK1


Mass: 43075.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1A1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P48729, non-specific serine/threonine protein kinase

-
Non-polymers , 7 types, 208 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#7: Chemical ChemComp-LCI / [4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium


Mass: 345.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26FN6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL ...Details: CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days.

-
Data collection

DiffractionMean temperature: 100.5 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.28→29.31 Å / Num. obs: 22991 / % possible obs: 98.1 % / Redundancy: 4 % / Rrim(I) all: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 2.28→2.4 Å / Num. unique obs: 3359 / Rrim(I) all: 0.56

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
REFMACphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQD

5fqd


Resolution: 2.28→29.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22117 1071 4.7 %RANDOM
Rwork0.17496 ---
obs0.17709 21917 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.28→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 141 190 2787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192723
X-RAY DIFFRACTIONr_bond_other_d00.022597
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9823617
X-RAY DIFFRACTIONr_angle_other_deg3.5852.9856018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43322.812128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34615483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5951522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022892
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02582
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3275.4951220
X-RAY DIFFRACTIONr_mcbond_other4.3255.4961221
X-RAY DIFFRACTIONr_mcangle_it6.2268.2311526
X-RAY DIFFRACTIONr_mcangle_other6.2248.2311527
X-RAY DIFFRACTIONr_scbond_it5.0566.0671503
X-RAY DIFFRACTIONr_scbond_other5.0556.0681504
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5158.8052088
X-RAY DIFFRACTIONr_long_range_B_refined9.95460.2022955
X-RAY DIFFRACTIONr_long_range_B_other9.94959.9462927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 79 -
Rwork0.254 1603 -
obs--99.23 %

+
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