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- PDB-2xs0: Linear binding motifs for JNK and for calcineurin antagonisticall... -

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Basic information

Entry
Database: PDB / ID: 2xs0
TitleLinear binding motifs for JNK and for calcineurin antagonistically control the nuclear shuttling of NFAT4
Components
  • MITOGEN-ACTIVATED PROTEIN KINASE 8
  • NUCLEAR FACTOR OF ACTIVATED T-CELLS, CYTOPLASMIC 3
KeywordsTRANSCRIPTION / TRANSFERASE / MAPK SIGNALING PATHWAYS / LINEAR BINDING MOTIFS
Function / homology
Function and homology information


positive regulation of artery morphogenesis / positive regulation of cell killing / JUN phosphorylation / Interleukin-38 signaling / negative regulation of vascular associated smooth muscle cell differentiation / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / DN4 thymocyte differentiation ...positive regulation of artery morphogenesis / positive regulation of cell killing / JUN phosphorylation / Interleukin-38 signaling / negative regulation of vascular associated smooth muscle cell differentiation / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / DN4 thymocyte differentiation / calcineurin-NFAT signaling cascade / WNT5:FZD7-mediated leishmania damping / positive thymic T cell selection / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / CLEC7A (Dectin-1) induces NFAT activation / DSCAM interactions / NRAGE signals death through JNK / positive regulation of cardiac muscle hypertrophy / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / Calcineurin activates NFAT / mitogen-activated protein kinase / regulation of macroautophagy / response to mechanical stimulus / response to UV / stress-activated MAPK cascade / protein serine/threonine kinase binding / JNK cascade / cellular response to cadmium ion / positive regulation of protein metabolic process / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / FCERI mediated Ca+2 mobilization / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of miRNA transcription / negative regulation of protein binding / FCERI mediated MAPK activation / peptidyl-threonine phosphorylation / regulation of circadian rhythm / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cellular response to reactive oxygen species / cellular response to mechanical stimulus / protein import into nucleus / regulation of protein localization / cellular senescence / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Signaling by ALK fusions and activated point mutants / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear factor of activated T cells (NFAT) / Mitogen-activated protein (MAP) kinase, JNK / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain ...Nuclear factor of activated T cells (NFAT) / Mitogen-activated protein (MAP) kinase, JNK / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Immunoglobulin E-set / 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 / Immunoglobulin-like fold / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 8 / Nuclear factor of activated T-cells, cytoplasmic 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBarkai, T. / Toeoroe, I. / Garai, A. / Remenyi, A.
CitationJournal: Sci. Signal / Year: 2012
Title: Specificity of Linear Motifs that Bind to a Common Mitogen-Activated Protein Kinase Docking Groove.
Authors: Garai, A. / Zeke, A. / Gogl, G. / Toro, I. / Fordos, F. / Blankenburg, H. / Barkai, T. / Varga, J. / Alexa, A. / Emig, D. / Albrecht, M. / Remenyi, A.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE 8
B: NUCLEAR FACTOR OF ACTIVATED T-CELLS, CYTOPLASMIC 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4533
Polymers45,9472
Non-polymers5061
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-8.9 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.530, 106.550, 130.910
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 MITOGEN-ACTIVATED PROTEIN KINASE 8 / MAP KINASE 8 / MAPK 8 / STRESS-ACTIVATED PROTEIN KINASE JNK1 / JNK1 / C-JUN N-TERMINAL KINASE 1 / ...MAP KINASE 8 / MAPK 8 / STRESS-ACTIVATED PROTEIN KINASE JNK1 / JNK1 / C-JUN N-TERMINAL KINASE 1 / JNK-46 / STRESS-ACTIVATED PROTEIN KINASE 1


Mass: 44206.059 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P45983, mitogen-activated protein kinase
#2: Protein/peptide NUCLEAR FACTOR OF ACTIVATED T-CELLS, CYTOPLASMIC 3 / NF-ATC3 / T-CELL TRANSCRIPTION FACTOR NFAT4 / NFATX


Mass: 1740.977 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF NFAT4, RESIDUES 141-154 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q12968
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 183 TO VAL ENGINEERED RESIDUE IN CHAIN A, TYR 185 TO PHE
Sequence detailsTHE SEQUENCE OF CHAIN A CORRESPONDS TO ISOFORM 3 OF THE UNIPROT ACCESSION ID P45983

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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: 2.64 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growpH: 8.5 / Details: 24-26% PEG1000, 100MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2010 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.9 Å / Num. obs: 13792 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 67.47 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.06 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XRW

2xrw


Resolution: 2.6→30.883 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 24.67 / Stereochemistry target values: ML
Details: RESIDUES -1,0,1-5, 174-187, 366-384 IN CHAIN A AND 141-142 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2457 1379 10 %
Rwork0.1879 --
obs0.1938 13785 99.83 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 56.59 Å2
Baniso -1Baniso -2Baniso -3
1-32.5003 Å20 Å20 Å2
2--17.022 Å20 Å2
3---13.6641 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 31 18 2952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043000
X-RAY DIFFRACTIONf_angle_d0.8114063
X-RAY DIFFRACTIONf_dihedral_angle_d18.6921175
X-RAY DIFFRACTIONf_chiral_restr0.057444
X-RAY DIFFRACTIONf_plane_restr0.003517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.37051400.32071227X-RAY DIFFRACTION100
2.6929-2.80060.33551300.2841217X-RAY DIFFRACTION100
2.8006-2.9280.30791360.26281216X-RAY DIFFRACTION100
2.928-3.08230.37261330.23751246X-RAY DIFFRACTION100
3.0823-3.27520.26311410.22211215X-RAY DIFFRACTION100
3.2752-3.52770.28611350.21221231X-RAY DIFFRACTION100
3.5277-3.88210.23111370.18371242X-RAY DIFFRACTION100
3.8821-4.44240.22131450.15791239X-RAY DIFFRACTION100
4.4424-5.59160.21111380.16011258X-RAY DIFFRACTION100
5.5916-30.88490.21641440.16651315X-RAY DIFFRACTION99
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)
13.1651-4.37511.84236.9771-2.60751.0764-0.02920.3803-0.1910.0236-0.26470.2835-0.3012-0.59340.28670.37160.2171-0.04610.5139-0.2280.5467-52.280119.1703-2.7399
20.19550.1007-0.04680.1587-0.10360.0797-0.07120.0727-0.0515-0.04260.06940.01590.07550.05940.01750.25430.0774-0.0627-0.0029-0.03960.2566-37.144214.4014-3.9582
30.07960.0017-0.01750.0014-0.00230.0955-0.1166-0.05820.04630.0455-0.0862-0.01710.10350.0378-0.04240.1961-0.07330.1510.00840.05520.3439-38.011811.82825.8017
40.0377-0.0228-0.04940.02470.03110.0653-0.02470.0549-0.02720.0133-0.01750.0060.0093-0.0491-0.01870.11810.08430.24410.0158-0.09990.0849-35.861116.400814.7493
50.00680.0042-0.04550.1746-0.03830.3374-0.0409-0.0112-0.0632-0.0766-0.11610.06910.06310.069-0.10950.1473-0.0250.07850.1108-0.04480.1663-32.270912.68134.6885
60.0058-0.0010.01750.12010.01090.0712-0.06820.0076-0.05170.1261-0.04150.03840.11110.106-0.07990.04460.11140.31020.0818-0.0525-0.1224-21.254414.424517.2037
70.97230.3917-0.26062.40410.45050.20760.1550.0746-0.4553-0.4046-0.05010.52940.49630.2053-0.13360.61430.21690.05830.3130.11310.3935-18.7042-1.097212.6987
80.0087-0.0271-0.01450.3234-0.05290.0453-0.0022-0.0337-0.0183-0.005-0.00170.00460.04650.00290.01360.28260.24080.09640.25720.23910.1993-18.35221.778622.9926
90.33690.5862-0.12931.1339-0.51990.7741-0.2762-0.1277-0.3301-0.3895-0.279-0.08260.53060.06020.40870.79330.2120.31590.39820.14940.5296-10.3308-4.966118.5341
102.98530.10330.07870.5161-1.6265.1822-0.330.0001-0.6262-0.3620.02391.02360.99870.12580.25171.15790.1176-0.06660.56510.31981.0983-16.1294-14.939229.2648
110.144-0.02570.00750.12660.06730.0436-0.1066-0.3116-0.11170.13860.0354-0.03640.11060.1154-0.01230.26030.32670.07550.54820.00950.1545-8.784512.175724.3219
120.24670.08310.10130.0541-0.00310.1318-0.0685-0.00160.06590.025-0.0766-0.01070.0881-0.0080.05510.2284-0.1020.14990.2187-0.08150.4008-47.09977.041716.54
130.41740.247-0.45070.7377-1.12392.13330.0080.06230.1421-0.11460.17690.05520.11-0.1228-0.12050.2044-0.05740.00920.21460.01120.1661-13.854327.196410.7789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:39)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 40:71)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 72:93)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 94:123)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 124:173)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 188:191)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 192:217)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 218:247)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 248:263)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 264:337)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 338:365)
13X-RAY DIFFRACTION13(CHAIN B)

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