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- PDB-6zqs: Crystal structure of double-phosphorylated p38alpha with ATF2(83-102) -

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Basic information

Entry
Database: PDB / ID: 6zqs
TitleCrystal structure of double-phosphorylated p38alpha with ATF2(83-102)
Components
  • Cyclic AMP-dependent transcription factor ATF-2
  • Mitogen-activated protein kinase 14
KeywordsTRANSCRIPTION / MAPK SIGNALING PATHWAYS
Function / homology
Function and homology information


abducens nucleus development / hypoglossal nucleus development / facial nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / growth plate cartilage chondrocyte differentiation / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of cardiac muscle myoblast proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process ...abducens nucleus development / hypoglossal nucleus development / facial nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / growth plate cartilage chondrocyte differentiation / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of cardiac muscle myoblast proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / cellular response to anisomycin / motor neuron apoptotic process / cAMP response element binding / leucine zipper domain binding / cAMP response element binding protein binding / histone H2B acetyltransferase activity / brainstem development / cellular response to leucine starvation / NK T cell differentiation / vacuole organization / neurofilament cytoskeleton organization / histone H4 acetyltransferase activity / hepatocyte apoptotic process / NGF-stimulated transcription / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / mitotic intra-S DNA damage checkpoint signaling / regulation of synaptic membrane adhesion / stress-induced premature senescence / positive regulation of myoblast fusion / cartilage condensation / stress-activated protein kinase signaling cascade / 3'-UTR-mediated mRNA stabilization / CD163 mediating an anti-inflammatory response / response to osmotic stress / positive regulation of cyclase activity / response to dietary excess / positive regulation of myotube differentiation / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of muscle cell differentiation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / white fat cell differentiation / Myogenesis / Platelet sensitization by LDL / NFAT protein binding / cellular response to lipoteichoic acid / regulation of cytokine production involved in inflammatory response / histone acetyltransferase activity / peptidyl-threonine phosphorylation / Activation of the AP-1 family of transcription factors / p38MAPK cascade / ERK/MAPK targets / MAP kinase kinase activity / hematopoietic progenitor cell differentiation / Regulation of MITF-M-dependent genes involved in pigmentation / cellular response to vascular endothelial growth factor stimulus / MAP kinase activity / BMP signaling pathway / mitogen-activated protein kinase / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / RHO GTPases Activate NADPH Oxidases / JNK cascade / negative regulation of hippo signaling / positive regulation of myoblast differentiation / Response of EIF2AK4 (GCN2) to amino acid deficiency / osteoclast differentiation / positive regulation of interleukin-12 production / cis-regulatory region sequence-specific DNA binding / signal transduction in response to DNA damage / p38MAPK events / negative regulation of angiogenesis / positive regulation of erythrocyte differentiation / in utero embryonic development / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / liver development / protein import into nucleus / transcription initiation-coupled chromatin remodeling / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / lipid metabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of DNA Repair Genes / cellular response to virus / activated TAK1 mediates p38 MAPK activation / Heme signaling / negative regulation of inflammatory response to antigenic stimulus / negative regulation of canonical Wnt signaling pathway / Transcriptional activation of mitochondrial biogenesis / promoter-specific chromatin binding / platelet activation / bone development / response to insulin / NOD1/2 Signaling Pathway / cellular senescence / VEGFA-VEGFR2 Pathway / mRNA transcription by RNA polymerase II / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation
Similarity search - Function
Transcription factor cyclic AMP-dependent, CRE-BP1-type / : / bZIP transcription factor / 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 kinase 14 / Mitogen-activated protein (MAP) kinase p38-like ...Transcription factor cyclic AMP-dependent, CRE-BP1-type / : / bZIP transcription factor / 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 kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / 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 / 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
Chem-3FF / Cyclic AMP-dependent transcription factor ATF-2 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsKirsch, K. / Sok, P. / Poti, A.L. / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: Cyclic AMP-dependent transcription factor ATF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3743
Polymers43,9492
Non-polymers4251
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-10 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.401, 84.602, 122.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-704-

HOH

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / ...MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / MAX-interacting protein 2 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / Stress-activated protein kinase 2a / SAPK2a


Mass: 41647.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A / Plasmid: PET DERIVATIVE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q16539, 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: 2301.463 Da / Num. of mol.: 1 / Mutation: S90N / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15336, histone acetyltransferase
#3: Chemical ChemComp-3FF / 2-[(2,4-difluorophenyl)amino]-7-{[(2R)-2,3-dihydroxypropyl]oxy}-10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-one


Mass: 425.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21F2NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG 3350, 0.1 M cacodylate ph 6.5

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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: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→69.62 Å / Num. obs: 30463 / % possible obs: 99.1 % / Redundancy: 12.5 % / Biso Wilson estimate: 38.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Net I/σ(I): 17.8 / Num. measured all: 380252 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-26.21.5991.118420.4250.6641.74488.2
8.94-69.6210.30.0361.539710.0090.03199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TCA

6tca


Resolution: 1.95→69.62 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 1502 4.94 %
Rwork0.1753 28878 -
obs0.1776 30380 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→69.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 31 351 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822988
X-RAY DIFFRACTIONf_angle_d1.08554070
X-RAY DIFFRACTIONf_chiral_restr0.0583456
X-RAY DIFFRACTIONf_plane_restr0.0056518
X-RAY DIFFRACTIONf_dihedral_angle_d17.4339407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.3638930.2842336X-RAY DIFFRACTION88.97
2.01-2.080.24771480.23122592X-RAY DIFFRACTION99.49
2.09-2.170.26661600.21012586X-RAY DIFFRACTION99.82
2.17-2.270.2291360.19682596X-RAY DIFFRACTION99.85
2.27-2.390.25031350.19362613X-RAY DIFFRACTION99.82
2.39-2.540.27831350.19442618X-RAY DIFFRACTION99.93
2.54-2.730.24941390.18312651X-RAY DIFFRACTION99.96
2.73-3.010.26281350.18072671X-RAY DIFFRACTION99.93
3.01-3.440.22011350.16452661X-RAY DIFFRACTION99.86
3.44-4.340.17541450.14652694X-RAY DIFFRACTION99.82
4.34-69.620.21421410.17292860X-RAY DIFFRACTION99.93
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)
16.88898831514-2.090076975941.552911918772.22122668572-2.239530229597.767169458860.244589516083-0.0814946983066-0.360869821311-0.380791647573-0.08913191623270.7383052969740.184064519387-0.736336309691-0.1597813466410.4216653344920.0306185851379-0.03484083589890.385134348504-0.07729835357860.385120909005-18.4458567376-31.1436192915-3.00931090359
21.02181407594-0.2861129049650.1294617057961.49703842747-0.3589671759862.538668939730.0550980256993-0.112592195351-0.01665381469340.0945804664874-0.002895726331320.02638756263010.0643215532903-0.0910078119136-0.04955901517590.250469851661-0.0481242686812-0.01182354489970.29701427034-0.03148686047390.276829472583-10.8985061464-32.074746689621.5872150906
32.5507088055-0.985264001507-0.4571118138391.113101474950.4767028005221.87432912035-0.140851637489-0.3013399127270.2177187419940.1931276376290.121934855623-0.3076232320320.1170862040650.0940549174734-0.01306776885970.331867620576-0.0225255452678-0.09493749483560.387977603929-0.03733868330340.346800327229-0.192115554885-35.638179961328.852651272
49.28240221903-1.2796527782-4.739818021567.297743777971.610704406986.678835952740.2262912101280.2665020436910.570317908971-0.426157596512-0.0144842899873-0.402583260168-0.459280255338-0.0547704588981-0.2485874179390.319404909903-0.005919290043520.01566904477010.2125889101480.03240428713420.298300697651-14.6584648065-14.11396206057.52013366166
56.804678221921.81957343491-2.207515572943.30613279294-3.26573140733.255620291280.091630682991-0.7287126378730.5108810069770.5969019122970.04518833137510.802185755421-0.011049290522-0.93435108395-0.2280448794620.535093828604-0.1081279180490.01027356514290.888023102773-0.02874498920590.505090680637-25.5235357991-31.385516345339.5738677176
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 47 )AA5 - 472 - 44
22chain 'A' and (resid 48 through 261 )AA48 - 26145 - 258
33chain 'A' and (resid 262 through 333 )AA262 - 333259 - 330
44chain 'A' and (resid 334 through 352 )AA334 - 352331 - 349
55chain 'B' and (resid 88 through 101 )BC88 - 1011 - 14

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