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- PDB-7xzr: Crystal structure of TNIK-AMPPNP-thiopeptide TP15 complex -

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Basic information

Entry
Database: PDB / ID: 7xzr
TitleCrystal structure of TNIK-AMPPNP-thiopeptide TP15 complex
Components
  • TRAF2 and NCK-interacting protein kinase
  • thiopeptide TP15
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
: / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / TRIETHYLENE GLYCOL / TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
Revision 1.4Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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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: TRAF2 and NCK-interacting protein kinase
C: thiopeptide TP15
D: thiopeptide TP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,45212
Polymers73,9534
Non-polymers1,4998
Water3,351186
1
A: TRAF2 and NCK-interacting protein kinase
C: thiopeptide TP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8497
Polymers36,9762
Non-polymers8735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-33 kcal/mol
Surface area14360 Å2
MethodPISA
2
B: TRAF2 and NCK-interacting protein kinase
D: thiopeptide TP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6035
Polymers36,9762
Non-polymers6273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-25 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.110, 167.650, 53.710
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein TRAF2 and NCK-interacting protein kinase


Mass: 35118.195 Da / Num. of mol.: 2
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 TP15


Type: Cyclic peptide / Class: Inhibitor / Mass: 1858.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002381

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Non-polymers , 5 types, 194 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: ammonium acetate, MgSO4, Hepes-Na, PEG smear medium

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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: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.26→43.34 Å / Num. obs: 41561 / % possible obs: 99.9 % / Redundancy: 45.3 % / CC1/2: 0.998 / Net I/σ(I): 11
Reflection shellResolution: 2.26→2.34 Å / Num. unique obs: 4174 / CC1/2: 0.507

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Processing

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

6ra7


Resolution: 2.26→43.34 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1957 4.71 %
Rwork0.182 --
obs0.184 41541 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 89 186 5314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095266
X-RAY DIFFRACTIONf_angle_d1.0227143
X-RAY DIFFRACTIONf_dihedral_angle_d13.703720
X-RAY DIFFRACTIONf_chiral_restr0.057764
X-RAY DIFFRACTIONf_plane_restr0.009904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.320.38171420.3522839X-RAY DIFFRACTION100
2.32-2.380.36111350.30012795X-RAY DIFFRACTION100
2.38-2.450.29991430.26322816X-RAY DIFFRACTION100
2.45-2.530.27411390.23452847X-RAY DIFFRACTION100
2.53-2.620.30491450.22562806X-RAY DIFFRACTION100
2.62-2.720.27731360.22872816X-RAY DIFFRACTION100
2.72-2.850.29711420.22432825X-RAY DIFFRACTION100
2.85-30.26341400.20972831X-RAY DIFFRACTION100
3-3.190.25771390.19832811X-RAY DIFFRACTION100
3.19-3.430.24261330.19612829X-RAY DIFFRACTION100
3.43-3.780.21011410.16522851X-RAY DIFFRACTION100
3.78-4.320.18131350.14132814X-RAY DIFFRACTION100
4.32-5.440.18991420.13612850X-RAY DIFFRACTION100
5.44-43.340.16461450.15252854X-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)
13.6844-0.17952.39972.9073-0.61873.8554-0.0726-0.1186-0.0599-0.06450.01960.37080.1043-0.27390.02270.35930.00830.0780.2756-0.09590.5141-13.240228.1101-2.0332
23.1759-0.06330.04782.06950.18882.3002-0.04870.14780.1443-0.1053-0.0612-0.2468-0.10620.33070.12420.2957-0.01670.05410.2789-0.03040.44785.156924.77261.0829
34.69151.6076-0.8713.8883-0.65341.8637-0.0365-0.2741-0.21640.378-0.0862-0.17990.1550.15420.12030.31630.0119-0.02370.3128-0.03060.28326.684511.258110.3008
44.94420.08251.21346.1581-5.62027.71020.05590.07420.91110.5895-0.2933-0.8654-1.32521.04190.22680.40230.007-0.00380.4242-0.09060.715416.440229.26722.8193
52.91490.3298-0.6382.3306-0.35831.7156-0.0993-0.1925-0.25930.1985-0.02280.02870.3724-0.02850.12060.64030.00190.10830.3731-0.04270.4105-1.6857-13.990711.8339
60.9333-0.048-0.13512.4421-0.39592.35720.05570.06380.0801-0.1012-0.085-0.493-0.08290.11640.01970.39560.00570.07720.27060.00110.426913.2863-23.2874-5.8776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 99 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 100 THROUGH 166 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 167 THROUGH 279 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 280 THROUGH 310 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 12 THROUGH 99 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 100 THROUGH 312 )

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