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- PDB-8ypf: The crystal structure of inactive p38 complexed with a ATF2 from ... -

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Basic information

Entry
Database: PDB / ID: 8ypf
TitleThe crystal structure of inactive p38 complexed with a ATF2 from 46 to 90
Components
  • Cyclic AMP-dependent transcription factor ATF-2
  • Mitogen-activated protein kinase 14
KeywordsTRANSFERASE / MAP KINASE P38 ALPHA / docking interactions
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 / leucine zipper domain binding / cAMP response element binding protein binding / histone H2B acetyltransferase activity / positive regulation of mitochondrial membrane permeability involved in apoptotic process / brainstem development / cellular response to leucine starvation / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / NK T cell differentiation / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / ADP signalling through P2Y purinoceptor 1 / Regulation of TP53 Activity through Phosphorylation / histone H4 acetyltransferase activity / vacuole organization / neurofilament cytoskeleton organization / apoptotic process involved in development / Myogenesis / NGF-stimulated transcription / VEGFA-VEGFR2 Pathway / intrinsic apoptotic signaling pathway in response to hypoxia / mitotic intra-S DNA damage checkpoint signaling / regulation of synaptic membrane adhesion / motor neuron apoptotic process / stress-induced premature senescence / response to osmotic stress / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / hepatocyte apoptotic process / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / D-glucose import / p38MAPK cascade / fatty acid oxidation / response to dietary excess / cellular response to lipoteichoic acid / response to muramyl dipeptide / outflow tract morphogenesis / white fat cell differentiation / peptidyl-threonine phosphorylation / Response of EIF2AK4 (GCN2) to amino acid deficiency / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / chondrocyte differentiation / adipose tissue development / vascular endothelial growth factor receptor signaling pathway / negative regulation of hippo signaling / positive regulation of myoblast differentiation / BMP signaling pathway / hematopoietic progenitor cell differentiation / positive regulation of DNA-binding transcription factor activity / histone acetyltransferase activity / stress-activated MAPK cascade / skeletal muscle tissue development / cis-regulatory region sequence-specific DNA binding / positive regulation of cardiac muscle cell proliferation / JNK cascade / positive regulation of brown fat cell differentiation / response to muscle stretch / striated muscle cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / transcription initiation-coupled chromatin remodeling / positive regulation of erythrocyte differentiation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / negative regulation of angiogenesis / placenta development / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / positive regulation of D-glucose import / cellular response to ionizing radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / stem cell differentiation / TP53 Regulates Transcription of DNA Repair Genes
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
Cyclic AMP-dependent transcription factor ATF-2 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y.Y. / Pei, C.J. / He, Q.Q. / Luo, Z.P. / Wu, J.W. / Wang, Z.X.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0802500 China
Ministry of Science and Technology (MoST, China)2022YFA0806504 China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into the allosteric activation of p38alpha MAP kinase via specific docking interactions
Authors: Zhang, Y.Y. / Pei, C.J. / He, Q.Q. / Luo, Z.P. / Wu, J.W. / Wang, Z.X.
History
DepositionMar 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)46,4172
Polymers46,4172
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.873, 81.873, 122.585
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAP kinase 14 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 41338.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, 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: 5078.776 Da / Num. of mol.: 1
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.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG1500, 0.1 M MMT buffer (DL-malic acid, MES monohydrate and Tris base, molar ratios 1:2:2) pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32662 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.24
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 3201 / CC1/2: 0.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.94 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2181 1535 4.82 %
Rwork0.1907 30312 -
obs0.1921 31847 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.77 Å2
Refinement stepCycle: LAST / Resolution: 2→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 0 230 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782824
X-RAY DIFFRACTIONf_angle_d0.89313829
X-RAY DIFFRACTIONf_chiral_restr0.0553430
X-RAY DIFFRACTIONf_plane_restr0.0079489
X-RAY DIFFRACTIONf_dihedral_angle_d13.10791049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.3272940.24712110X-RAY DIFFRACTION75.25
2.07-2.140.24481430.23762701X-RAY DIFFRACTION97.5
2.14-2.220.26391810.21752746X-RAY DIFFRACTION99.56
2.22-2.330.25791500.21452804X-RAY DIFFRACTION99.86
2.33-2.450.25451380.21312772X-RAY DIFFRACTION99.93
2.45-2.60.2361930.21842850X-RAY DIFFRACTION99.97
2.6-2.80.21961490.19492832X-RAY DIFFRACTION100
2.8-3.080.23521250.20862835X-RAY DIFFRACTION99.73
3.08-3.530.21211490.19112843X-RAY DIFFRACTION99.97
3.53-4.450.19351770.15722836X-RAY DIFFRACTION99.77
4.45-40.940.17931360.16352983X-RAY DIFFRACTION98.83

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