[English] 日本語
Yorodumi
- PDB-7qra: Crystal structure of CK1 delta in complex with VN725 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qra
TitleCrystal structure of CK1 delta in complex with VN725
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / kinase / CK1d / inhibitor
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / endoplasmic reticulum-Golgi intermediate compartment membrane / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / : / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cilium / ciliary basal body / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-EYI / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChaikuad, A. / Nemec, V. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity.
Authors: Nemec, V. / Khirsariya, P. / Janovska, P. / Moyano, P.M. / Maier, L. / Prochazkova, P. / Kebkova, P. / Gybel', T. / Berger, B.T. / Chaikuad, A. / Reinecke, M. / Kuster, B. / Knapp, S. / Bryja, V. / Paruch, K.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: 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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,72228
Polymers137,6994
Non-polymers3,02324
Water5,999333
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2608
Polymers34,4251
Non-polymers8357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3229
Polymers34,4251
Non-polymers8978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1016
Polymers34,4251
Non-polymers6775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0395
Polymers34,4251
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.208, 84.949, 90.070
Angle α, β, γ (deg.)70.840, 74.080, 86.930
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 294 / Label seq-ID: 5 - 296

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D


Mass: 34424.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-EYI / 4-[3-cyclohexyl-5-(4-fluorophenyl)imidazol-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine


Mass: 360.427 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H21FN4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.1M sodium sulfate, 0.1M citrate 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.74 Å / Num. obs: 48143 / % possible obs: 92.9 % / Redundancy: 2.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.097 / Rrim(I) all: 0.172 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.532.80.3762.273460.8450.3070.53996.6
7.59-49.743.20.05115990.9970.0330.06297.4

-
Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RU8

6ru8


Resolution: 2.4→49.74 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.859 / SU B: 23.3 / SU ML: 0.273 / SU R Cruickshank DPI: 0.7347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 2272 4.7 %RANDOM
Rwork0.2385 ---
obs0.2406 45677 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.99 Å2 / Biso mean: 32.3 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20.64 Å20.07 Å2
2--2.17 Å2-1.66 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.4→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9270 0 198 333 9801
Biso mean--33.23 27.28 -
Num. residues----1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0149664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178714
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.66112980
X-RAY DIFFRACTIONr_angle_other_deg0.811.65620388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27651128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49420.821536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.574151742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1991582
X-RAY DIFFRACTIONr_chiral_restr0.0580.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021904
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95640.05
12B95640.05
21A90280.07
22C90280.07
31A90360.07
32D90360.07
41B90370.07
42C90370.07
51B90320.07
52D90320.07
61C92450.05
62D92450.05
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 177 -
Rwork0.296 3550 -
all-3727 -
obs--96.03 %
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)
10.2746-0.2976-0.34720.44250.40861.06330.0360.03680.0213-0.01570.0087-0.0549-0.0429-0.1075-0.04480.05550.02210.01510.0828-0.04180.04415.7024-8.3968-14.7087
20.30580.30420.42490.32980.41061.19470.0555-0.0304-0.01790.01840.0101-0.03720.1001-0.1098-0.06550.0686-0.04340.00480.0869-0.04690.046410.176719.5184-50.8545
35.5830.7204-0.58421.0583-0.35341.6337-0.0152-0.07680.5125-0.07860.0390.06050.17650.4152-0.02380.02240.03650.00520.1677-0.04780.099238.4866-30.9579-65.3456
40.30450.0405-0.30220.40420.76791.94860.10920.04160.03250.01420.0809-0.0801-0.09450.0983-0.19020.05720.01130.01820.0913-0.07070.071318.7555-22.9738-50.1184
50.99950.41860.78760.25720.0042.00530.04760.1482-0.19630.03310.0707-0.1079-0.05850.2059-0.11840.0168-0.03230.01320.1498-0.11580.103734.520439.9144-6.3736
60.8019-0.0826-0.1250.18750.60882.30930.10760.0153-0.05180.00150.0333-0.06660.1196-0.0633-0.14090.0729-0.0388-0.00250.1017-0.06820.068920.256331.0435-18.5357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 294
2X-RAY DIFFRACTION2B3 - 294
3X-RAY DIFFRACTION3C3 - 81
4X-RAY DIFFRACTION4C82 - 294
5X-RAY DIFFRACTION5D3 - 176
6X-RAY DIFFRACTION6D177 - 294

+
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