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- PDB-6y8h: Novel p38-alpha crystal lattice with highly exposed p38/TAB1 non-... -

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Basic information

Entry
Database: PDB / ID: 6y8h
TitleNovel p38-alpha crystal lattice with highly exposed p38/TAB1 non-canonical PPI surface.
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / FBDD / FRAGMENT BASED DRUG DESIGN / P38 / MAPK14 / KINASE
Function / homology
Function and homology information


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 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence ...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 / 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 / Myogenesis / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / cartilage condensation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / JUN kinase activity / mitogen-activated protein kinase / negative regulation of hippo signaling / chondrocyte differentiation / positive regulation of myoblast differentiation / vascular endothelial growth factor receptor signaling pathway / skeletal muscle tissue development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / Neutrophil degranulation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / positive regulation of D-glucose import / stem cell differentiation / response to insulin / placenta development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / bone development / cellular response to virus / positive regulation of protein import into nucleus / glucose metabolic process / spindle pole / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / kinase activity / MAPK cascade / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / angiogenesis / response to lipopolysaccharide / transcription by RNA polymerase II / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SB4 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsDe Nicola, G.F. / Nichols, C.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
British Heart FoundationSP/14/2/30922, FS/14/29/30896 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17164 United Kingdom
CitationJournal: To Be Published
Title: Novel p38-alpha crystal lattice with highly exposed p38/TAB1 non-canonical PPI surface.
Authors: De Nicola, G.F. / Nichols, C.E.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9329
Polymers41,3221
Non-polymers6108
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-54 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.864, 102.325, 103.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-405-

CA

21A-660-

HOH

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Components

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


Mass: 41322.098 Da / Num. of mol.: 1 / Mutation: C162S
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: Chemical ChemComp-SB4 / 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE / SB220025


Mass: 338.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19FN6
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG400, 5% PEG550-MME, 0.1M CALCIUM ACETATE, 0.1M MES PH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.37→51.16 Å / Num. obs: 90228 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 1 / Net I/σ(I): 10.6
Reflection shellResolution: 1.37→1.39 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4412 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
DIALSdata collection
PHENIX1.16_3549refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A9U

1a9u


Resolution: 1.37→51.16 Å / SU ML: 0.2296 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 31.0897
RfactorNum. reflection% reflection
Rfree0.2402 8499 4.88 %
Rwork0.2185 --
obs0.2196 90144 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.79 Å2
Refinement stepCycle: LAST / Resolution: 1.37→51.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 32 248 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542923
X-RAY DIFFRACTIONf_angle_d0.82773984
X-RAY DIFFRACTIONf_chiral_restr0.0771444
X-RAY DIFFRACTIONf_plane_restr0.0044514
X-RAY DIFFRACTIONf_dihedral_angle_d3.18591729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.46142660.46465488X-RAY DIFFRACTION98.19
1.39-1.40.47813120.44575436X-RAY DIFFRACTION99.67
1.4-1.420.4512940.43085525X-RAY DIFFRACTION99.71
1.42-1.440.41163170.41365491X-RAY DIFFRACTION99.66
1.44-1.460.37333020.39275496X-RAY DIFFRACTION99.64
1.46-1.480.37812790.37765509X-RAY DIFFRACTION99.66
1.48-1.50.36312830.35695539X-RAY DIFFRACTION99.66
1.5-1.520.36362500.35115578X-RAY DIFFRACTION99.66
1.52-1.540.34672630.33675554X-RAY DIFFRACTION99.59
1.54-1.570.35022800.31855507X-RAY DIFFRACTION99.31
1.57-1.60.30372720.3065452X-RAY DIFFRACTION99.38
1.6-1.620.29583160.28675530X-RAY DIFFRACTION99.39
1.62-1.660.25232800.27655487X-RAY DIFFRACTION99.57
1.66-1.690.27373520.26715479X-RAY DIFFRACTION99.61
1.69-1.730.33363010.27135512X-RAY DIFFRACTION99.78
1.73-1.770.30272710.28615519X-RAY DIFFRACTION99.74
1.77-1.810.30242880.25175577X-RAY DIFFRACTION99.86
1.81-1.860.27142680.23175535X-RAY DIFFRACTION99.83
1.86-1.910.24132560.21465544X-RAY DIFFRACTION99.76
1.91-1.980.252750.20685527X-RAY DIFFRACTION99.69
1.98-2.050.23292880.20435523X-RAY DIFFRACTION99.73
2.05-2.130.22933260.20795500X-RAY DIFFRACTION99.81
2.13-2.230.21062800.19845534X-RAY DIFFRACTION99.91
2.23-2.340.20673040.19745523X-RAY DIFFRACTION99.81
2.34-2.490.23432200.20415563X-RAY DIFFRACTION99.86
2.49-2.680.22872800.20375590X-RAY DIFFRACTION99.98
2.68-2.950.19072730.20235534X-RAY DIFFRACTION99.93
2.95-3.380.22982780.19145565X-RAY DIFFRACTION100
3.38-4.260.17362310.16195559X-RAY DIFFRACTION99.4
4.26-51.160.19592940.17055547X-RAY DIFFRACTION99.98

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