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- PDB-7xzq: Crystal structure of TNIK-thiopeptide TP1 complex -

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Basic information

Entry
Database: PDB / ID: 7xzq
TitleCrystal structure of TNIK-thiopeptide TP1 complex
Components
  • TRAF2 and NCK-interacting protein kinase
  • thiopeptide TP1
KeywordsSIGNALING PROTEIN/INHIBITOR / ripp / thiopeptide / kinase inhibition / complex / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome ...microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome / Wnt signaling pathway / MAPK cascade / presynapse / actin cytoskeleton organization / Oxidative Stress Induced Senescence / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / 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. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / 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
Similarity search - Domain/homology
: / 1,4-BUTANEDIOL / TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsHamada, K. / Vinogradov, A.A. / Zhang, Y. / Chang, J.S. / Nishimura, H. / Goto, Y. / Onaka, H. / Suga, H. / Ogata, K. / Sengoku, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
Authors: Vinogradov, A.A. / Zhang, Y. / Hamada, K. / Chang, J.S. / Okada, C. / Nishimura, H. / Terasaka, N. / Goto, Y. / Ogata, K. / Sengoku, T. / Onaka, H. / Suga, H.
History
DepositionJun 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: 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 1.2Nov 23, 2022Group: 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 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAF2 and NCK-interacting protein kinase
B: thiopeptide TP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3457
Polymers36,8942
Non-polymers4515
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-6 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.290, 152.840, 98.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TRAF2 and NCK-interacting protein kinase


Mass: 35118.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIK, KIAA0551 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase
#2: Protein/peptide thiopeptide TP1


Type: Cyclic peptide / Class: Inhibitor / Mass: 1776.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002379
#3: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Hepes-Na, NaCl, 1,4-butanediol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.09→49.48 Å / Num. obs: 24396 / % possible obs: 99.9 % / Redundancy: 29.9 % / CC1/2: 0.998 / Net I/σ(I): 12.68
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 2401 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RA7

6ra7


Resolution: 2.09→49.48 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1915 7.86 %
Rwork0.196 --
obs0.201 24372 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 30 132 2697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092617
X-RAY DIFFRACTIONf_angle_d0.9733522
X-RAY DIFFRACTIONf_dihedral_angle_d15.168363
X-RAY DIFFRACTIONf_chiral_restr0.053372
X-RAY DIFFRACTIONf_plane_restr0.011450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.45881330.40391575X-RAY DIFFRACTION100
2.14-2.20.34161350.33491577X-RAY DIFFRACTION100
2.2-2.260.34711340.28261563X-RAY DIFFRACTION100
2.27-2.340.33861360.26171585X-RAY DIFFRACTION100
2.34-2.420.30221360.2331594X-RAY DIFFRACTION100
2.42-2.520.25011360.22061588X-RAY DIFFRACTION100
2.52-2.630.25341350.20861580X-RAY DIFFRACTION100
2.63-2.770.28451350.20811597X-RAY DIFFRACTION100
2.77-2.950.26331370.20151601X-RAY DIFFRACTION100
2.95-3.170.23091360.2061596X-RAY DIFFRACTION100
3.17-3.490.22441370.19361616X-RAY DIFFRACTION100
3.49-40.23491380.17341619X-RAY DIFFRACTION100
4-5.030.22841410.14911641X-RAY DIFFRACTION100
5.04-49.480.23021460.16681725X-RAY DIFFRACTION100
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)
17.89891.0213-6.81193.61010.55448.5382-0.0794-0.1325-0.0328-0.0688-0.00520.0831-0.1441-0.19640.07370.2303-0.0208-0.06260.3680.0210.34236.994523.8239-14.9403
24.9711-0.45670.52841.2825-0.79261.28090.14930.1622-0.02620.0096-0.0650.20210.0586-0.1943-0.07250.28160.00230.02720.3018-0.01920.36213.647722.8728-8.089
33.74010.3308-0.83413.5048-0.55421.91070.1814-0.41740.03130.3931-0.1916-0.0143-0.09520.08350.01450.2822-0.07390.02170.29530.01790.239727.581819.6815.8914
44.920.17030.59452.65592.56092.6377-0.05640.37250.6379-0.2311-0.1207-0.1525-0.44530.21470.14310.3723-0.08980.08280.39210.11720.536237.268627.4675-8.0596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 11 THROUGH 59 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 60 THROUGH 126 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 127 THROUGH 279 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 280 THROUGH 310 )

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