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- PDB-2zoq: Structural dissection of human mitogen-activated kinase ERK1 -

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Basic information

Entry
Database: PDB / ID: 2zoq
TitleStructural dissection of human mitogen-activated kinase ERK1
ComponentsMitogen-activated protein kinase 3
KeywordsTRANSFERASE / serine/threonine kinase / ERK1 / Acetylation / ATP-binding / Cell cycle / Host-virus interaction / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of xenophagy / xenophagy / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / response to epidermal growth factor ...positive regulation of xenophagy / xenophagy / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of cellular pH / positive regulation of macrophage proliferation / positive regulation of cyclase activity / outer ear morphogenesis / Regulation of the apoptosome activity / cartilage development / regulation of Golgi inheritance / interleukin-1-mediated signaling pathway / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / Activation of the AP-1 family of transcription factors / face development / MAPK3 (ERK1) activation / ERK/MAPK targets / pseudopodium / RUNX2 regulates osteoblast differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / Advanced glycosylation endproduct receptor signaling / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / mitogen-activated protein kinase / phosphatase binding / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / Signal attenuation / BMP signaling pathway / Schwann cell development / stress-activated MAPK cascade / Growth hormone receptor signaling / peptidyl-tyrosine autophosphorylation / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / sensory perception of pain / negative regulation of TORC1 signaling / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / cellular response to amino acid starvation / myelination / RNA Polymerase I Promoter Opening / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / caveola / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / modulation of chemical synaptic transmission / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / ISG15 antiviral mechanism / cellular response to reactive oxygen species / cellular response to mechanical stimulus / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants
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
Chem-5ID / Mitogen-activated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKinoshita, T. / Tada, T. / Nakae, S. / Yoshida, I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of human mono-phosphorylated ERK1 at Tyr204
Authors: Kinoshita, T. / Yoshida, I. / Nakae, S. / Okita, K. / Gouda, M. / Matsubara, M. / Yokota, K. / Ishiguro, H. / Tada, T.
History
DepositionJun 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 3
B: Mitogen-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0788
Polymers87,0562
Non-polymers1,0226
Water5,657314
1
A: Mitogen-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0394
Polymers43,5281
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0394
Polymers43,5281
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.382, 91.540, 64.930
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase 3 / Extracellular signal-regulated kinase 1 / ERK-1 / Insulin-stimulated MAP2 kinase / MAP kinase 1 / ...Extracellular signal-regulated kinase 1 / ERK-1 / Insulin-stimulated MAP2 kinase / MAP kinase 1 / MAPK 1 / p44-ERK1 / ERT2 / p44-MAPK / Microtubule-associated protein 2 kinase


Mass: 43527.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK3, ERK1, PRKM3 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P27361, mitogen-activated protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13IN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M ammonium sulphate, 2% polyethyleneglycol400, 0.1M, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 28758 / Num. obs: 28700 / % possible obs: 99.8 % / Observed criterion σ(I): 144275 / Redundancy: 5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERK

1erk
PDB Unreleased entry


Resolution: 2.39→45.57 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.267 1435 -
Rwork0.249 --
all-28700 -
obs-27265 99.8 %
Refinement stepCycle: LAST / Resolution: 2.39→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 0 52 314 6102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6

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