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- PDB-4h36: Crystal Structure of JNK3 in Complex with ATF2 Peptide -

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Basic information

Entry
Database: PDB / ID: 4h36
TitleCrystal Structure of JNK3 in Complex with ATF2 Peptide
Components
  • Cyclic AMP-dependent transcription factor ATF-2
  • Mitogen-activated protein kinase 10
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / cellular response to anisomycin / positive regulation of transforming growth factor beta2 production ...abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / cellular response to anisomycin / positive regulation of transforming growth factor beta2 production / cAMP response element binding / leucine zipper domain binding / cellular lipid metabolic process / cAMP response element binding protein binding / histone H2B acetyltransferase activity / positive regulation of mitochondrial membrane permeability involved in apoptotic process / cellular response to leucine starvation / JUN kinase activity / brainstem development / NK T cell differentiation / neurofilament cytoskeleton organization / vacuole organization / histone H4 acetyltransferase activity / apoptotic process involved in development / NGF-stimulated transcription / intrinsic apoptotic signaling pathway in response to hypoxia / mitotic intra-S DNA damage checkpoint signaling / motor neuron apoptotic process / response to osmotic stress / hepatocyte apoptotic process / Activation of the AP-1 family of transcription factors / outflow tract morphogenesis / p38MAPK cascade / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / white fat cell differentiation / response to light stimulus / mitogen-activated protein kinase / cis-regulatory region sequence-specific DNA binding / adipose tissue development / BMP signaling pathway / hematopoietic progenitor cell differentiation / histone acetyltransferase activity / JNK cascade / transcription initiation-coupled chromatin remodeling / negative regulation of angiogenesis / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / liver development / Regulation of PTEN gene transcription / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptidyl-threonine phosphorylation / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / response to organic cyclic compound / cellular response to virus / positive regulation of DNA-binding transcription factor activity / RNA polymerase II transcription regulator complex / protein import into nucleus / cellular senescence / sequence-specific double-stranded DNA binding / rhythmic process / Circadian Clock / site of double-strand break / HATs acetylate histones / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of protein phosphorylation / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein phosphorylation / protein serine kinase activity / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Transcription factor cyclic AMP-dependent, CRE-BP1-type / bZIP transcription factor / Mitogen-activated protein (MAP) kinase, JNK / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...Transcription factor cyclic AMP-dependent, CRE-BP1-type / bZIP transcription factor / Mitogen-activated protein (MAP) kinase, JNK / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / 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
Cyclic AMP-dependent transcription factor ATF-2 / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNwachukwu, J.C. / Laughlin, J.D. / Figuera-Losada, M. / Cherry, L. / Nettles, K.W. / LoGrasso, P.V.
CitationJournal: Structure / Year: 2012
Title: Structural Mechanisms of Allostery and Autoinhibition in JNK Family Kinases.
Authors: Laughlin, J.D. / Nwachukwu, J.C. / Figuera-Losada, M. / Cherry, L. / Nettles, K.W. / Lograsso, P.V.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Jun 17, 2015Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 10
B: Cyclic AMP-dependent transcription factor ATF-2


Theoretical massNumber of molelcules
Total (without water)42,2172
Polymers42,2172
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-10 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.580, 84.580, 127.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Mitogen-activated protein kinase 10 / MAP kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / ...MAP kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3


Mass: 41180.641 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 45-400)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JNK3, JNK3A, MAPK10, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Protein/peptide Cyclic AMP-dependent transcription factor ATF-2 / cAMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / Cyclic AMP- ...cAMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / Cyclic AMP-responsive element-binding protein 2 / CREB-2 / cAMP-responsive element-binding protein 2 / HB16 / cAMP response element-binding protein CRE-BP1


Mass: 1036.267 Da / Num. of mol.: 1 / Fragment: UNP residues 48-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATF2, CREB2, CREBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15336
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris, 28-31% PEG3350, pH 5.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.17 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.17 Å / Relative weight: 1
ReflectionResolution: 3→40.126 Å / Num. all: 10972 / Num. obs: 10970 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3-3.07185.3
3.07-3.16187.2
3.16-3.26191.4
3.26-3.38190.9
3.38-3.52194.5
3.52-3.68197
3.68-3.87195.6
3.87-4.11197.6
4.11-4.43198.6
4.43-4.87198.7
4.87-5.58198.6
5.58-7.02199.3
7.02-40.13199.1

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Processing

Software
NameVersionClassification
Blu-Iceicedata collection
PHENIX(phenix.automr: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JNK

1jnk


Resolution: 3→40.126 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 528 4.81 %RANDOM
Rwork0.2163 ---
obs0.2188 10970 99.99 %-
all-10972 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.742 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7147 Å2-0 Å20 Å2
2---2.7147 Å2-0 Å2
3---5.4294 Å2
Refinement stepCycle: LAST / Resolution: 3→40.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 0 4 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032930
X-RAY DIFFRACTIONf_angle_d0.8453983
X-RAY DIFFRACTIONf_dihedral_angle_d16.1141084
X-RAY DIFFRACTIONf_chiral_restr0.061449
X-RAY DIFFRACTIONf_plane_restr0.004512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30190.33691330.28552546X-RAY DIFFRACTION100
3.3019-3.77930.28171340.22742572X-RAY DIFFRACTION100
3.7793-4.76040.21511420.17992594X-RAY DIFFRACTION100
4.7604-40.12940.2851190.21262731X-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)
15.0065-1.03791.2047.49723.75335.8646-0.5726-0.6690.23030.10660.57190.8076-0.4746-0.8182-0.25550.35890.1045-0.16930.5998-0.0610.3587-52.305622.4258-9.5284
21.05550.2973-0.62571.6019-0.25060.3797-0.0834-0.0688-0.1226-0.0892-0.2032-0.02420.14380.0428-0.150.45140.1298-0.13120.20840.01980.2219-43.02418.2385-8.0143
30.9345-0.34730.77241.0038-0.20630.65340.00360.02120.0533-0.1934-0.05580.0717-0.1299-0.10660.00590.44220.1668-0.14090.3433-0.06490.2279-39.726623.8069-14.8001
40.9729-0.23270.05561.13351.29091.56910.1495-0.1822-0.09290.3699-0.04680.02660.3079-0.1021-0.03230.43030.0255-0.04720.12520.01450.1757-39.896522.3411.6904
53.39160.3787-2.38030.4790.4172.7702-0.0451-0.0029-0.09730.0848-0.2408-0.13680.18940.18250.12260.35920.1832-0.00530.25040.00760.1764-31.427431.31620.7458
60.9668-0.72550.90552.36160.4812.9443-0.1211-0.24990.01560.2294-0.00730.3169-0.069-0.60730.21830.28870.0933-0.0990.1891-0.08250.1468-45.206427.5924-1.6582
70.48040.5409-0.00771.3455-0.16540.03080.04470.2681-0.2981-0.1606-0.0945-0.19790.18380.1424-0.00130.66170.33430.04170.4496-0.03840.3159-15.892717.3401-14.0556
80.9712-0.45450.30511.3532-0.22960.32710.24420.1952-0.0148-0.0801-0.16870.07360.1720.1699-0.03230.19870.10960.00360.17910.07650.1961-16.926229.2581-4.4118
92.30860.48040.98512.17510.73480.55420.13160.1305-0.0728-0.156-0.14530.01240.122-0.017-0.0590.26160.1062-0.14380.1814-0.10820.0693-22.669624.0493-10.1781
100.37380.752-0.47872.1769-1.26270.75020.2338-0.0844-0.31330.30260.01020.0630.28240.0089-0.10280.7795-0.065-0.08880.72270.13230.6825-28.967319.91831.8213
112.8992-1.3693-2.85075.1534-2.39096.34450.19730.3741-0.1385-0.5549-0.22090.2280.4424-0.2788-0.06060.80160.3022-0.0260.3852-0.06940.1117-17.727613.83071.8932
120.8353-0.45040.18640.9011-0.61241.10380.04380.11510.20920.09180.1203-0.0179-0.1456-0.0520.01970.13820.2267-0.00850.315-0.0370.2615-11.782525.57418.1005
130.3127-0.1048-0.27670.63390.61350.69960.03890.0394-0.0884-0.02770.01080.01630.13410.10070.12490.45310.5642-0.01930.39960.04380.3047-8.740216.9298-6.8008
140.1365-0.15480.04280.2547-0.06410.0771-0.00550.0253-0.05340.02390.04420.08750.0592-0.01220.29430.67730.50450.10020.3470.03930.2398-8.273412.07577.3819
150.0289-0.0799-0.06630.01750.05090.0860.05620.22110.0072-0.013-0.1192-0.10090.11370.2892-0.24330.1771.1450.03270.6448-0.02220.19080.464718.23226.0585
161.051-0.4643-0.07081.90450.8530.47650.2712-0.0040.0946-0.25740.056-0.42670.09860.4759-0.21240.2770.16720.07590.47930.09790.256-2.942128.6708-2.4915
171.63380.3376-0.50910.1058-0.06940.2020.27960.01670.464-0.0385-0.06160.0033-0.38820.4355-0.18270.41170.14540.17960.64650.22870.3469-12.300537.2545-10.7155
186.47621.9169-3.40091.4057-1.25072.76790.0872-0.7761-0.10060.54860.14910.52390.0843-0.5018-0.21790.72650.06190.13790.47090.00890.4391-29.171836.898310.7426
193.042-1.39951.10776.86330.68684.6861-0.2009-0.0980.3940.0912-0.07660.0398-0.3755-0.10220.09690.5441-0.0269-0.05260.2895-0.12020.29-42.277631.139417.1276
202.024-0.51540.36892.8212.18472.29910.12050.22870.1216-0.3152-0.0770.0032-0.303-0.0294-0.15470.37160.08370.06830.2775-0.11520.1695-44.355434.10965.7771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 45:52)
2X-RAY DIFFRACTION2(chain A and resid 53:76)
3X-RAY DIFFRACTION3(chain A and resid 77:87)
4X-RAY DIFFRACTION4(chain A and resid 88:103)
5X-RAY DIFFRACTION5(chain A and resid 104:126)
6X-RAY DIFFRACTION6(chain A and resid 127:148)
7X-RAY DIFFRACTION7(chain A and resid 149:164)
8X-RAY DIFFRACTION8(chain A and resid 165:192)
9X-RAY DIFFRACTION9(chain A and resid 193:207)
10X-RAY DIFFRACTION10(chain A and resid 208:220)
11X-RAY DIFFRACTION11(chain A and resid 222:229)
12X-RAY DIFFRACTION12(chain A and resid 230:249)
13X-RAY DIFFRACTION13(chain A and resid 250:259)
14X-RAY DIFFRACTION14(chain A and resid 260:276)
15X-RAY DIFFRACTION15(chain A and resid 277:326)
16X-RAY DIFFRACTION16(chain A and resid 327:354)
17X-RAY DIFFRACTION17(chain A and resid 355:373)
18X-RAY DIFFRACTION18(chain A and resid 374:383)
19X-RAY DIFFRACTION19(chain A and resid 384:389)
20X-RAY DIFFRACTION20(chain A and resid 390:400)

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