[English] 日本語
Yorodumi
- PDB-7zhq: Crystal structure of TTBK1 in complex with compound 10 (7-009) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zhq
TitleCrystal structure of TTBK1 in complex with compound 10 (7-009)
ComponentsTau-tubulin kinase 1
KeywordsTRANSFERASE / kinase / ttbk1 / tau tubulin kinase 1 / inhibitor complex
Function / homology
Function and homology information


positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation ...positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / learning or memory / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tau-tubulin kinase 1, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Tau-tubulin kinase 1, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-IRD / PHOSPHATE ION / Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChaikuad, A. / Axtman, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis.
Authors: Bashore, F.M. / Marquez, A.B. / Chaikuad, A. / Howell, S. / Dunn, A.S. / Beltran, A.A. / Smith, J.L. / Drewry, D.H. / Beltran, A.S. / Axtman, A.D.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tau-tubulin kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,51512
Polymers35,5151
Non-polymers1,00011
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint23 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.308, 39.543, 49.650
Angle α, β, γ (deg.)90.000, 103.230, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Tau-tubulin kinase 1 / Brain-derived tau kinase


Mass: 35515.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK1, BDTK, KIAA1855 / Plasmid: pSumo-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IRD / (3~{S})-1-(4-azanyl-3,5,12-triazatetracyclo[9.7.0.0^{2,7}.0^{13,18}]octadeca-1(11),2,4,6,13(18),14,16-heptaen-16-yl)-3-methyl-pent-1-yn-3-ol


Mass: 346.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 14-23% PEG 3350, 0.2 M sodium acetate pH 7.0 and 0.1 M tris pH 7.5-9.0
PH range: 7.5-9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.8→48.33 Å / Num. obs: 30388 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 13.4 / Num. measured all: 203072
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.866.40.8581891929610.8290.3640.9342100
6.97-48.336.50.03437095720.9990.0140.03744.199.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q8W

7q8w


Resolution: 1.8→48.33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1988 / WRfactor Rwork: 0.1625 / FOM work R set: 0.8451 / SU B: 5.483 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1217 / SU Rfree: 0.1177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1493 4.9 %RANDOM
Rwork0.1738 ---
obs0.1757 28895 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.3 Å2 / Biso mean: 25.998 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0.21 Å2
2--2.11 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.8→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 67 183 2635
Biso mean--32.35 31.43 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172468
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.6543397
X-RAY DIFFRACTIONr_angle_other_deg1.3681.5975668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64420.903144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64915470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 111 -
Rwork0.254 2099 -
all-2210 -
obs--100 %
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)
13.67910.8403-0.08282.6938-0.1061.79350.0914-0.27070.28270.1615-0.04930.1635-0.1541-0.0692-0.04210.06050.01120.00260.1368-0.01730.030671.267439.14419.9181
22.04790.3296-0.08460.94360.07651.58520.00230.2145-0.0912-0.10520.02390.01160.02430.0647-0.02630.01330.0041-0.00450.0409-0.01950.009959.921831.2818-11.1397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 101
2X-RAY DIFFRACTION2A102 - 313

+
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