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- PDB-5umo: STRUCTURE OF EXTRACELLULAR SIGNAL-REGULATED KINASE -

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Basic information

Entry
Database: PDB / ID: 5umo
TitleSTRUCTURE OF EXTRACELLULAR SIGNAL-REGULATED KINASE
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / kinase / erk2
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 / ESR-mediated signaling / Regulation of the apoptosome activity / Interferon gamma signaling / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / FCERI mediated MAPK activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / Recycling pathway of L1 / neural crest cell development / 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 / regulation of cellular pH / positive regulation of macrophage proliferation / outer ear morphogenesis / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / Neutrophil degranulation / trachea formation / regulation of cytoskeleton organization / regulation of early endosome to late endosome transport / cellular response to organic substance / regulation of stress-activated MAPK cascade / positive regulation of macrophage chemotaxis / response to exogenous dsRNA / lung morphogenesis / ERBB2-ERBB3 signaling pathway / face development / androgen receptor signaling pathway / pseudopodium / progesterone receptor signaling pathway / positive regulation of telomere capping / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / decidualization / steroid hormone mediated signaling pathway / regulation of ossification / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / stress-activated MAPK cascade / Schwann cell development / sensory perception of pain / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / ERK1 and ERK2 cascade / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / 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 / positive regulation of translation / thymus development / positive regulation of peptidyl-threonine phosphorylation / response to nicotine / long-term synaptic potentiation
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
Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SIRAS / molecular replacement / Resolution: 2.26 Å
AuthorsCHLEBOWICZ, J. / ZHANG, F. / GOLDSMITH, E.J.
CitationJournal: Nature / Year: 1994
Title: Atomic structure of the MAP kinase ERK2 at 2.3 A resolution.
Authors: Zhang, F. / Strand, A. / Robbins, D. / Cobb, M.H. / Goldsmith, E.J.
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _software.name
SupersessionNov 22, 2017ID: 1ERK
Revision 1.2Nov 22, 2017Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Apr 13, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,2552
Polymers42,1591
Non-polymers961
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.320, 72.420, 61.250
Angle α, β, γ (deg.)90.000, 109.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42159.434 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 BL21(DE3) (bacteria)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 18% PEG 8,000, 0.2 M (NH4)2SO4, 50 mM MES, 5 mM DTT, 0.1 mM NaN3, pH 5.9

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 29, 1995
RadiationMonochromator: Cu-Kalpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→21.18 Å / Num. obs: 16950 / % possible obs: 97 % / Redundancy: 3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.8.0155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
Sir2014phasing
DENZOdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.26→21.18 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / Matrix type: sparse / SU B: 5.411 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.212
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 861 5.2 %RANDOM
Rwork0.1471 ---
obs0.1498 15799 87.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.72 Å2 / Biso mean: 38.626 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.01 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.26→21.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 5 175 3005
Biso mean--61.87 42.25 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192897
X-RAY DIFFRACTIONr_bond_other_d0.0020.022785
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9733928
X-RAY DIFFRACTIONr_angle_other_deg0.94736417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86624.214140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5315513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9861517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.261-2.3190.27150.179236138318.1490.152
2.319-2.3820.221430.185800134262.8170.161
2.382-2.450.25590.1731129132389.7960.152
2.45-2.5250.234540.181060125288.9780.16
2.525-2.6060.219680.1581063125590.120.14
2.606-2.6960.262570.1621048122690.1310.145
2.696-2.7960.232610.151983115290.6250.135
2.796-2.9080.227460.1641009113393.1160.15
2.908-3.0350.261550.153980107096.7290.142
3.035-3.180.203360.157976101699.6060.146
3.18-3.3480.21600.15192699199.4950.142
3.348-3.5450.193610.14784891599.3440.142
3.545-3.7830.199490.1484690199.3340.143
3.783-4.0750.185440.12276681499.5090.121
4.075-4.4470.116340.12571875599.6030.127
4.447-4.9450.166320.1176566881000.121
4.945-5.6590.181300.1475856151000.157
5.659-6.810.245270.165105371000.168
6.81-9.1690.181190.1374004191000.162
9.169-21.1760.151110.14826028196.4410.161

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