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- PDB-6zr5: Crystal structure of JNK1 in complex with ATF2(19-58) -

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Basic information

Entry
Database: PDB / ID: 6zr5
TitleCrystal structure of JNK1 in complex with ATF2(19-58)
Components
  • Cyclic AMP-dependent transcription factor ATF-2
  • Mitogen-activated protein kinase 8
KeywordsTRANSCRIPTION / MAPK SIGNALING PATHWAYS
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 / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin ...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 / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin / cAMP response element binding / JUN phosphorylation / positive regulation of cell killing / leucine zipper domain binding / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / brown fat cell proliferation / basal dendrite / cAMP response element binding protein binding / histone H2B acetyltransferase activity / positive regulation of mitochondrial membrane permeability involved in apoptotic process / JUN kinase activity / brainstem development / Activation of BIM and translocation to mitochondria / positive regulation of protein localization to mitochondrion / cellular response to leucine starvation / NK T cell differentiation / WNT5:FZD7-mediated leishmania damping / apoptotic process involved in development / vacuole organization / neurofilament cytoskeleton organization / histone H4 acetyltransferase activity / NGF-stimulated transcription / positive regulation of cyclase activity / intrinsic apoptotic signaling pathway in response to hypoxia / histone deacetylase regulator activity / mitotic intra-S DNA damage checkpoint signaling / motor neuron apoptotic process / response to osmotic stress / peptidyl-threonine phosphorylation / NRAGE signals death through JNK / histone acetyltransferase activity / Activation of the AP-1 family of transcription factors / hepatocyte apoptotic process / Fc-epsilon receptor signaling pathway / p38MAPK cascade / temperature homeostasis / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of protein metabolic process / outflow tract morphogenesis / white fat cell differentiation / : / mitogen-activated protein kinase / regulation of macroautophagy / adipose tissue development / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of protein binding / BMP signaling pathway / response to mechanical stimulus / hematopoietic progenitor cell differentiation / stress-activated MAPK cascade / response to UV / cis-regulatory region sequence-specific DNA binding / JNK cascade / energy homeostasis / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / NRIF signals cell death from the nucleus / transcription initiation-coupled chromatin remodeling / negative regulation of angiogenesis / cellular response to amino acid starvation / Regulation of PTEN gene transcription / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / peptidyl-serine phosphorylation / negative regulation of autophagy / protein serine/threonine kinase binding / integrin-mediated signaling pathway / FCERI mediated MAPK activation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to reactive oxygen species / lipid metabolic process / TP53 Regulates Transcription of DNA Repair Genes / Heme signaling / promoter-specific chromatin binding / liver development / cellular response to mechanical stimulus / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / cellular response to virus / mRNA transcription by RNA polymerase II / autophagy / RNA polymerase II transcription regulator complex / histone deacetylase binding / protein import into nucleus / sequence-specific double-stranded DNA binding / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / MAPK cascade / regulation of protein localization / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
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 / Basic-leucine zipper domain superfamily / Mitogen-activated protein (MAP) kinase, conserved site ...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 / Basic-leucine zipper domain superfamily / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cyclic AMP-dependent transcription factor ATF-2 / Mitogen-activated protein kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsKirsch, K. / Zeke, A. / Remenyi, A.
Funding support Hungary, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)NN 114309 Hungary
National Research Development and Innovation Office (NKFIH)KKP 126963 Hungary
CitationJournal: Nat Commun / Year: 2020
Title: Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38.
Authors: Kirsch, K. / Zeke, A. / Toke, O. / Sok, P. / Sethi, A. / Sebo, A. / Kumar, G.S. / Egri, P. / Poti, A.L. / Gooley, P. / Peti, W. / Bento, I. / Alexa, A. / Remenyi, A.
History
DepositionJul 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 8
C: Cyclic AMP-dependent transcription factor ATF-2
B: Mitogen-activated protein kinase 8
D: Cyclic AMP-dependent transcription factor ATF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47612
Polymers93,2364
Non-polymers1,2408
Water2,252125
1
A: Mitogen-activated protein kinase 8
C: Cyclic AMP-dependent transcription factor ATF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2386
Polymers46,6182
Non-polymers6204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-27 kcal/mol
Surface area18050 Å2
MethodPISA
2
B: Mitogen-activated protein kinase 8
D: Cyclic AMP-dependent transcription factor ATF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2386
Polymers46,6182
Non-polymers6204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-30 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.225, 110.400, 77.634
Angle α, β, γ (deg.)90.000, 94.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 402 or (resid 4 through 5...
21(chain B and (resid 402 through 16 or (resid 17...
12(chain C and (resid 22 through 39 or (resid 40...
22(chain D and (resid 22 through 25 or (resid 26...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 402 or (resid 4 through 5...A402
121(chain A and (resid 402 or (resid 4 through 5...A4 - 5
131(chain A and (resid 402 or (resid 4 through 5...A3 - 362
141(chain A and (resid 402 or (resid 4 through 5...A3 - 362
151(chain A and (resid 402 or (resid 4 through 5...A3 - 362
161(chain A and (resid 402 or (resid 4 through 5...A3 - 362
211(chain B and (resid 402 through 16 or (resid 17...B402 - 16
221(chain B and (resid 402 through 16 or (resid 17...B17
231(chain B and (resid 402 through 16 or (resid 17...B4 - 362
241(chain B and (resid 402 through 16 or (resid 17...B4 - 362
251(chain B and (resid 402 through 16 or (resid 17...B4 - 362
261(chain B and (resid 402 through 16 or (resid 17...B4 - 362
112(chain C and (resid 22 through 39 or (resid 40...C22 - 39
122(chain C and (resid 22 through 39 or (resid 40...C40
132(chain C and (resid 22 through 39 or (resid 40...C22 - 60
142(chain C and (resid 22 through 39 or (resid 40...C22 - 60
152(chain C and (resid 22 through 39 or (resid 40...C22 - 60
162(chain C and (resid 22 through 39 or (resid 40...C22 - 60
212(chain D and (resid 22 through 25 or (resid 26...D22 - 25
222(chain D and (resid 22 through 25 or (resid 26...D26
232(chain D and (resid 22 through 25 or (resid 26...D19 - 60
242(chain D and (resid 22 through 25 or (resid 26...D19 - 60
252(chain D and (resid 22 through 25 or (resid 26...D19 - 60
262(chain D and (resid 22 through 25 or (resid 26...D19 - 60

NCS ensembles :
ID
1
2

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Components

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

#1: Protein Mitogen-activated protein kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase ...MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 42032.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / Plasmid: PET DERIVATIVE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
References: UniProt: P45983, 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 / cAMP-responsive element-binding protein 2 / HB16 / Histone acetyltransferase ATF2 / cAMP response element-binding protein CRE-BP1


Mass: 4585.252 Da / Num. of mol.: 2 / Mutation: Q34R, H47R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATF2, CREB2, CREBP1 / Plasmid: PET DERIVATIVE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15336, histone acetyltransferase

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Non-polymers , 4 types, 133 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 10% PEG 20000, 20% PEG MME550, 0.03M MgCl2, 0.03M CaCl2, 0.1 M bicine/Trizma base, pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 100K-M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.699→44.943 Å / Num. obs: 23961 / % possible obs: 91.4 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.054 / Rrim(I) all: 0.082 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.699-2.833.20.432.430510.8680.3760.57387.2
8.95-44.943.60.03925.35980.9940.0330.05283.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XS0, 1BHI

2xs0

1bhi


Resolution: 2.699→44.943 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1185 4.95 %
Rwork0.182 22746 -
obs0.1856 23931 90.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.22 Å2 / Biso mean: 82.7472 Å2 / Biso min: 28.56 Å2
Refinement stepCycle: final / Resolution: 2.699→44.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 68 125 6152
Biso mean--49.64 66.33 -
Num. residues----781
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2088X-RAY DIFFRACTION10.015TORSIONAL
12B2088X-RAY DIFFRACTION10.015TORSIONAL
21C208X-RAY DIFFRACTION10.015TORSIONAL
22D208X-RAY DIFFRACTION10.015TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6992-2.8220.39161440.3129269486
2.822-2.97070.39241640.2827293194
2.9707-3.15680.34791380.2394296194
3.1568-3.40050.29811470.2249292793
3.4005-3.74250.24931490.1808294293
3.7425-4.28370.21211490.1536286291
4.2837-5.39560.22141480.1467274187
5.3956-44.9430.23321460.1653268884
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)
19.7214-0.9029-3.64972.69781.82832.41260.4090.303-0.08690.0250.056-0.24980.2287-0.3447-0.39410.53570.0135-0.02220.3934-0.0440.3641-32.947511.5898-4.2642
21.8126-0.0959-0.26452.673-3.52547.91710.07880.06050.017-0.0042-0.0333-0.07830.12780.0398-0.10210.33720.0003-0.00830.3225-0.02160.3955-33.999115.73612.748
35.10310.79660.43824.0989-0.95354.2866-0.2254-0.38050.45220.49520.17770.1737-0.7425-0.5484-0.03530.65190.1658-0.05880.6506-0.04280.4046-42.972215.234431.495
45.9149-4.3232-4.28964.1644.00573.8741-0.1299-0.63920.61010.32930.2635-0.812-0.48890.8602-0.33770.736-0.0733-0.13080.57580.08030.7349-32.002534.10154.5912
55.67550.89124.2929.49891.62733.36-0.0053-0.5295-0.12390.2667-0.23870.1164-0.2752-0.19010.41180.3641-0.04590.02550.60540.02680.3813-61.71567.902212.8456
62.4375-0.32431.9762.9096-1.55879.09190.08830.0725-0.00620.0051-0.0831-0.0610.13250.50180.0260.2784-0.00610.02270.5160.01260.4349-62.90413.7985-4.1577
75.50520.66342.22874.4795-0.17365.07720.09760.0472-0.2435-0.2590.063-0.11030.29040.271-0.11890.50880.05890.00150.44980.01460.3124-73.33772.9153-21.9323
82.62711.3804-1.46819.53813.48778.79270.36730.7279-0.11020.2759-0.4434-0.17151.15250.64470.14740.84550.0213-0.06510.76170.13030.7402-60.1759-14.67834.363
98.73030.29585.01918.588-0.22627.8370.3856-0.7097-1.53260.7257-0.0751-0.49050.51770.5861-0.1450.650.10030.00460.72060.11570.8113-20.8389-2.635923.7163
104.21-5.6069-2.92418.00842.68234.51730.79880.29410.5709-0.9259-0.4986-0.6751-0.0020.4164-0.23580.8042-0.0865-0.16120.88910.17960.9311-47.639521.2514-16.6574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:55)A6 - 55
2X-RAY DIFFRACTION2(chain A and resid 56:168)A56 - 168
3X-RAY DIFFRACTION3(chain A and resid 169:341)A169 - 341
4X-RAY DIFFRACTION4(chain A and resid 342:365)A342 - 365
5X-RAY DIFFRACTION5(chain B and resid 6:55)B6 - 55
6X-RAY DIFFRACTION6(chain B and resid 56:168)B56 - 168
7X-RAY DIFFRACTION7(chain B and resid 169:341)B169 - 341
8X-RAY DIFFRACTION8(chain B and resid 342:365)B342 - 365
9X-RAY DIFFRACTION9(chain C)C)0
10X-RAY DIFFRACTION10(chain D)D)0

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