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

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Basic information

Entry
Database: PDB / ID: 2xrw
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 / MAPK SIGNALING PATHWAYS / LINEAR BINDING MOTIF
Function / homology
Function and homology information


positive regulation of artery morphogenesis / cellular response to stress / positive regulation of cell killing / negative regulation of vascular associated smooth muscle cell differentiation / JUN phosphorylation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / : ...positive regulation of artery morphogenesis / cellular response to stress / positive regulation of cell killing / negative regulation of vascular associated smooth muscle cell differentiation / JUN phosphorylation / regulation of DNA replication origin binding / Interleukin-38 signaling / 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 / protein serine/threonine kinase binding / positive thymic T cell selection / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / CLEC7A (Dectin-1) induces NFAT activation / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / Calcineurin activates NFAT / MAP kinase activity / regulation of macroautophagy / mitogen-activated protein kinase / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / JNK cascade / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of protein metabolic process / 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 / cellular response to reactive oxygen species / cellular response to mechanical stimulus / histone deacetylase binding / rhythmic process / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / cellular senescence / sequence-specific double-stranded DNA binding / 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 / protein phosphatase binding / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to oxidative stress / cellular response to lipopolysaccharide / 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 / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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 / Stress-activated protein kinase JNK / 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: 1.33 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 23, 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)45,2065
Polymers44,5152
Non-polymers6903
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-14 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.230, 94.130, 47.840
Angle α, β, γ (deg.)90.00, 110.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE 8 / JNK1 / MITOGEN-ACTIVATED PROTEIN KINASE 8 ISOFORM JNK1 BETA2 / MITOGEN-ACTIVATED PROTEIN KINASE 8\ ...JNK1 / MITOGEN-ACTIVATED PROTEIN KINASE 8 ISOFORM JNK1 BETA2 / MITOGEN-ACTIVATED PROTEIN KINASE 8\ / ISOFORM CRA_D / CDNA FLJ77387\ / HIGHLY SIMILAR TO HOMO SAPIENS MITOGEN-ACTIVATED PROTEIN KINASE 8 (MAPK8)\ / TRANSCRIPT VARIANT 4\ / MRNA


Mass: 42774.355 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-364
Source method: isolated from a genetically manipulated source
Details: LAST 20 RESIDUES TRUNCATED / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: A1L4K2, UniProt: P45983*PLUS, mitogen-activated protein kinase
#2: Protein/peptide NUCLEAR FACTOR OF ACTIVATED T-CELLS\, CYTOPLASMIC 3 / PEPNFAT4 / NF-ATC3 / NFATC3 / T-CELL TRANSCRIPTION FACTOR NFAT4 / NF-AT4 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAMPPNP (ANP): THE GAMMA-PHOSPHATE GROUP IS NOT MODELLED.

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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: 2.35 Å3/Da / Density % sol: 47.59 % / Description: NONE
Crystal growpH: 5.5
Details: 18-20% PEG 8000, 100 MM SODIUM CITRATE PH 5.5, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2010 / Details: TOROIDAL MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→47.07 Å / Num. obs: 86996 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.45
Reflection shellResolution: 1.33→1.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.98 / % possible all: 99.3

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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 1UKH

1ukh


Resolution: 1.33→25.689 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 19.43 / Stereochemistry target values: ML
Details: RESIDUES 0, 173-188, 366-370 IN CHAIN A, RESIDUES 141-142 IN CHAIN B ARE COMPLETELY DISORDERED. THE AMPPNP RESIDUE IS PARTIALLY DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1866 1997 2.3 %
Rwork0.1651 --
obs0.1656 86986 99.38 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.457 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.3821 Å20 Å23.3077 Å2
2---4.8365 Å20 Å2
3---2.7231 Å2
Refinement stepCycle: LAST / Resolution: 1.33→25.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 39 422 3374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113071
X-RAY DIFFRACTIONf_angle_d1.3574166
X-RAY DIFFRACTIONf_dihedral_angle_d17.3431211
X-RAY DIFFRACTIONf_chiral_restr0.075455
X-RAY DIFFRACTIONf_plane_restr0.008530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.36320.34291480.29065978X-RAY DIFFRACTION99
1.3632-1.40010.24151410.25446095X-RAY DIFFRACTION100
1.4001-1.44130.25651390.23056091X-RAY DIFFRACTION100
1.4413-1.48780.20171460.20766098X-RAY DIFFRACTION100
1.4878-1.5410.22311360.19526095X-RAY DIFFRACTION100
1.541-1.60270.19281460.18216061X-RAY DIFFRACTION100
1.6027-1.67560.21381480.17236064X-RAY DIFFRACTION100
1.6756-1.76390.17511440.16196116X-RAY DIFFRACTION100
1.7639-1.87440.18971360.15816067X-RAY DIFFRACTION100
1.8744-2.01910.19061490.15286114X-RAY DIFFRACTION100
2.0191-2.22210.16221400.15156106X-RAY DIFFRACTION100
2.2221-2.54340.1771440.14746133X-RAY DIFFRACTION100
2.5434-3.20350.17411480.15896111X-RAY DIFFRACTION100
3.2035-25.69380.18111320.15975860X-RAY DIFFRACTION94
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)
10.6582-0.4776-0.24630.6931-0.52421.59450.3077-0.18840.14520.01220.1050.20070.16130.2793-0.38550.3898-0.07540.01710.3999-0.04570.49532.37130.53223.5885
20.6095-0.3120.16151.1932-0.26731.04010.0378-0.34560.13650.0693-0.1043-0.10520.0911-0.0124-0.00040.2236-0.0314-0.0240.322-0.1040.211821.763814.502628.0762
30.50020.30370.24630.4082-0.00090.24180.0153-0.13160.00390.0437-0.14570.10570.0166-0.19330.10480.152-0.0021-0.01270.258-0.0760.225317.726714.825519.6056
40.42460.31530.21960.23910.10250.26640.1629-0.07070.36050.0856-0.0693-0.2253-0.01130.2492-0.08260.15540.0172-0.00230.2307-0.00870.32279.349317.821410.1233
50.69880.1085-0.00760.36250.00520.4123-0.0278-0.24880.1468-0.0609-0.0095-0.01810.0110.04640.02440.14070.0019-0.0170.1683-0.04450.163214.655912.480219.8753
60.7991-0.4456-0.17991.12720.89321.21380.0826-0.07420.0906-0.04650.0314-0.06710.04710.0657-0.10810.15080.0038-0.00250.14270.0050.13642.4892.63628.4693
73.3932-0.82110.3932.3729-0.86212.8551-0.18480.1537-0.021-0.18210.1413-0.24970.46950.4285-0.01080.2210.05490.01390.2195-0.02610.20538.5913-12.8802-1.1362
82.42030.3597-1.6181.32630.51311.6232-0.30830.6052-0.3469-0.43850.0633-0.15070.4019-0.34110.19510.37480.03170.0970.29630.04650.205511.1767-7.3693-13.6505
90.215-0.0391-0.06430.0446-0.00870.0885-0.0960.0238-0.4494-0.4239-0.0873-0.45190.15830.06980.17860.3334-0.00960.15230.1783-0.00810.44884.9197-16.716-4.7098
100.87391.34430.1832.5924-0.63751.6801-0.1626-0.3118-0.13380.02320.15990.4370.1912-0.4716-0.02360.2158-0.02930.0520.32650.04570.2605-13.893-10.912712.0761
111.2193-0.2219-0.26570.4141-0.23830.48150.09470.09530.1268-0.1755-0.12320.0391-0.0266-0.070.0090.17320.0178-0.00280.14960.00690.1535-4.97857.09853.1688
120.8615-0.1893-0.16120.2623-0.33760.94130.23320.09290.4243-0.1715-0.074-0.0779-0.4246-0.1625-0.08080.21350.059-0.01220.2139-0.00250.243922.9122.49776.434
131.97110.726-0.15340.8030.50440.58650.16-0.29190.37630.1814-0.1450.06270.1535-0.1782-0.04110.2297-0.02880.03070.25410.03580.1994-8.37454.256625.4101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:6)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 7:38)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 39:68)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 69:85)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 86:123)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 124:226)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 227:246)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 247:258)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 259:272)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 273:293)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 294:341)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 342:365)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 143:154)

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