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- PDB-3qyz: Crystal structure of ERK2 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 3qyz
TitleCrystal structure of ERK2 in complex with an inhibitor
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING CELL CYCLE / PHOSPHORYLATION / Protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / Recycling pathway of L1 / neural crest cell development / diadenosine tetraphosphate biosynthetic process / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / : / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / progesterone receptor signaling pathway / androgen receptor signaling pathway / pseudopodium / negative regulation of cell differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / steroid hormone receptor signaling pathway / decidualization / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / sensory perception of pain / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / ERK1 and ERK2 cascade / cellular response to amino acid starvation / myelination / dendrite cytoplasm / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / caveola / positive regulation of translation / long-term synaptic potentiation / animal organ morphogenesis
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / 5'-azido-8-bromo-5'-deoxyadenosine / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 1.46 Å
AuthorsGelin, M. / Pochet, S. / Hoh, F. / Pirochi, M. / Guichou, J.-F. / Ferrer, J.-L. / Labesse, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: In-plate protein crystallization, in situ ligand soaking and X-ray diffraction.
Authors: le Maire, A. / Gelin, M. / Pochet, S. / Hoh, F. / Pirocchi, M. / Guichou, J.F. / Ferrer, J.L. / Labesse, G.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,73616
Polymers42,2361
Non-polymers1,50115
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.689, 70.237, 59.482
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 42235.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Production host: Escherichia coli (E. coli)
References: UniProt: P63086, mitogen-activated protein kinase

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Non-polymers , 5 types, 463 molecules

#2: Chemical ChemComp-Z8B / 5'-azido-8-bromo-5'-deoxyadenosine


Mass: 371.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrN8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG MME 2000, 0.1M MES, 0.1M ammonium sulfate, 0.02M beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2008
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.46→46.17 Å / Num. obs: 62817 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.46→1.54 Å / % possible all: 73.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Isomorphous replacement / Resolution: 1.46→46.166 Å / SU ML: 0.19 / σ(F): 1.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 5599 5.02 %RANDOM
Rwork0.1614 ---
all0.175 ---
obs0.1631 62817 85.97 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89.749 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7486 Å20 Å2-1.226 Å2
2--0.8558 Å20 Å2
3----2.7315 Å2
Refinement stepCycle: LAST / Resolution: 1.46→46.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 80 448 3306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083089
X-RAY DIFFRACTIONf_angle_d1.0924179
X-RAY DIFFRACTIONf_dihedral_angle_d16.0741214
X-RAY DIFFRACTIONf_chiral_restr0.074473
X-RAY DIFFRACTIONf_plane_restr0.006517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.47660.43031170.41971884X-RAY DIFFRACTION46
1.4766-1.4940.39731140.36812131X-RAY DIFFRACTION52
1.494-1.51220.39351340.3372423X-RAY DIFFRACTION58
1.5122-1.53130.33551320.30692631X-RAY DIFFRACTION63
1.5313-1.55150.3371370.29112822X-RAY DIFFRACTION69
1.5515-1.57280.29061740.28173036X-RAY DIFFRACTION74
1.5728-1.59520.3181810.24263231X-RAY DIFFRACTION79
1.5952-1.6190.26092040.23393431X-RAY DIFFRACTION84
1.619-1.64430.25551830.21323540X-RAY DIFFRACTION87
1.6443-1.67130.2381920.19733715X-RAY DIFFRACTION89
1.6713-1.70010.23922040.19143804X-RAY DIFFRACTION94
1.7001-1.7310.22511940.16793955X-RAY DIFFRACTION94
1.731-1.76430.20671950.16453798X-RAY DIFFRACTION95
1.7643-1.80030.19852020.15054020X-RAY DIFFRACTION96
1.8003-1.83950.20911710.13733948X-RAY DIFFRACTION96
1.8395-1.88230.20431860.12933971X-RAY DIFFRACTION96
1.8823-1.92930.17591820.14113927X-RAY DIFFRACTION95
1.9293-1.98150.20061910.14083916X-RAY DIFFRACTION95
1.9815-2.03980.1731670.1453896X-RAY DIFFRACTION94
2.0398-2.10570.18182140.14163853X-RAY DIFFRACTION94
2.1057-2.18090.1662470.13873774X-RAY DIFFRACTION93
2.1809-2.26820.15891960.14223832X-RAY DIFFRACTION93
2.2682-2.37150.20492250.14573778X-RAY DIFFRACTION92
2.3715-2.49650.22912140.1513788X-RAY DIFFRACTION92
2.4965-2.65290.17472340.15083713X-RAY DIFFRACTION92
2.6529-2.85770.2072150.16663856X-RAY DIFFRACTION93
2.8577-3.14520.18542050.16093788X-RAY DIFFRACTION93
3.1452-3.60020.17911800.1463831X-RAY DIFFRACTION93
3.6002-4.53520.1332110.1353856X-RAY DIFFRACTION94
4.5352-46.18930.21381980.17823871X-RAY DIFFRACTION94

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