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- PDB-8ygw: The Crystal Structure of MAPK11 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8ygw
TitleThe Crystal Structure of MAPK11 from Biortus
ComponentsMitogen-activated protein kinase 11
KeywordsTRANSCRIPTION / Kinase / Serine/threonine-protein kinase / Transferase / Stress response / Transcription regulation / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


negative regulation of cardiac muscle cell proliferation / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cardiac muscle cell proliferation / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cellular response to UV-B / positive regulation of muscle cell differentiation / Myogenesis / Activation of the AP-1 family of transcription factors ...negative regulation of cardiac muscle cell proliferation / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cardiac muscle cell proliferation / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cellular response to UV-B / positive regulation of muscle cell differentiation / Myogenesis / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events / positive regulation of interleukin-12 production / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / bone development / cellular response to virus / VEGFA-VEGFR2 Pathway / osteoblast differentiation / cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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-B96 / Mitogen-activated protein kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of MAPK11 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
History
DepositionFeb 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9352
Polymers41,4071
Non-polymers5281
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.061, 61.860, 147.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 11 / MAP kinase 11 / MAPK 11 / Mitogen-activated protein kinase p38 beta / MAP kinase p38 beta / p38b / ...MAP kinase 11 / MAPK 11 / Mitogen-activated protein kinase p38 beta / MAP kinase p38 beta / p38b / Stress-activated protein kinase 2b / SAPK2b / p38-2


Mass: 41407.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK11, PRKM11, SAPK2, SAPK2B / Production host: Escherichia coli (E. coli)
References: UniProt: Q15759, mitogen-activated protein kinase
#2: Chemical ChemComp-B96 / 1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA


Mass: 527.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H37N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH6.5, 28% PEGMME2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95374 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 3.3→49.15 Å / Num. obs: 5815 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 9.3
Reflection shellResolution: 3.3→3.57 Å / Rmerge(I) obs: 0.827 / Num. unique obs: 1159

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.301→49.15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.878 / SU B: 35.3 / SU ML: 0.538 / Cross valid method: FREE R-VALUE / ESU R Free: 0.654
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2781 284 4.913 %
Rwork0.2054 5496 -
all0.209 --
obs-5780 99.948 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 78.808 Å2
Baniso -1Baniso -2Baniso -3
1--2.978 Å20 Å20 Å2
2--7.254 Å2-0 Å2
3----4.276 Å2
Refinement stepCycle: LAST / Resolution: 3.301→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 39 26 2697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0122732
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162513
X-RAY DIFFRACTIONr_angle_refined_deg0.6851.6493705
X-RAY DIFFRACTIONr_angle_other_deg0.2391.5625850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2815323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.609522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10710473
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.80110130
X-RAY DIFFRACTIONr_chiral_restr0.0320.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.1790.2598
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.22597
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21363
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.211
X-RAY DIFFRACTIONr_nbd_other0.1570.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.24
X-RAY DIFFRACTIONr_mcbond_it2.0498.2021301
X-RAY DIFFRACTIONr_mcbond_other2.0488.2031301
X-RAY DIFFRACTIONr_mcangle_it3.60612.3021621
X-RAY DIFFRACTIONr_mcangle_other3.60612.3021622
X-RAY DIFFRACTIONr_scbond_it1.5988.261431
X-RAY DIFFRACTIONr_scbond_other1.5978.2571432
X-RAY DIFFRACTIONr_scangle_it2.86212.3332084
X-RAY DIFFRACTIONr_scangle_other2.86112.3312085
X-RAY DIFFRACTIONr_lrange_it6.091103.5643126
X-RAY DIFFRACTIONr_lrange_other6.09103.5543127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.301-3.3860.35150.277378X-RAY DIFFRACTION100
3.386-3.4780.339310.275388X-RAY DIFFRACTION100
3.478-3.5780.34390.274386X-RAY DIFFRACTION100
3.578-3.6880.291140.275361X-RAY DIFFRACTION100
3.688-3.8080.344210.241349X-RAY DIFFRACTION100
3.808-3.9410.225170.233350X-RAY DIFFRACTION99.7283
3.941-4.0890.347140.21328X-RAY DIFFRACTION100
4.089-4.2540.33170.195318X-RAY DIFFRACTION100
4.254-4.4420.294200.188311X-RAY DIFFRACTION100
4.442-4.6570.253200.17285X-RAY DIFFRACTION100
4.657-4.9060.266180.185293X-RAY DIFFRACTION100
4.906-5.20.19190.176266X-RAY DIFFRACTION100
5.2-5.5540.196120.175259X-RAY DIFFRACTION100
5.554-5.9920.273100.196228X-RAY DIFFRACTION100
5.992-6.5540.258140.208237X-RAY DIFFRACTION100
6.554-7.310.34160.163190X-RAY DIFFRACTION100
7.31-8.4080.27120.172181X-RAY DIFFRACTION100
8.408-10.2170.36650.151168X-RAY DIFFRACTION100
10.217-14.1250.13980.145128X-RAY DIFFRACTION100
14.125-49.150.30220.32892X-RAY DIFFRACTION100

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