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- PDB-6d5y: Crystal structure of ERK2 G169D mutant -

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Basic information

Entry
Database: PDB / ID: 6d5y
TitleCrystal structure of ERK2 G169D mutant
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cytosine metabolic process / cardiac neural crest cell development involved in heart development / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis ...phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cytosine metabolic process / cardiac neural crest cell development involved in heart development / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / RSK activation / ERKs are inactivated / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / outer ear morphogenesis / : / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / Signaling by LTK in cancer / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / ERBB signaling pathway / trachea formation / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / positive regulation of neuroinflammatory response / Frs2-mediated activation / Activation of the AP-1 family of transcription factors / ERBB2-ERBB3 signaling pathway / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / ERK/MAPK targets / MAPK1 (ERK2) activation / regulation of cytoskeleton organization / positive regulation of macrophage chemotaxis / face development / Bergmann glial cell differentiation / Recycling pathway of L1 / thyroid gland development / positive regulation of telomere maintenance / pseudopodium / lung morphogenesis / Advanced glycosylation endproduct receptor signaling / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of cell differentiation / Signal attenuation / RHO GTPases Activate WASPs and WAVEs / Growth hormone receptor signaling / Schwann cell development / stress-activated MAPK cascade / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / Nuclear events stimulated by ALK signaling in cancer / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ciliary tip / thymus development / cellular response to amino acid starvation / Regulation of PTEN gene transcription / chemokine-mediated signaling pathway / Signal transduction by L1 / B cell receptor signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / positive regulation of cholesterol biosynthetic process / MAP2K and MAPK activation / Negative Regulation of CDH1 Gene Transcription / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / caveola / cellular response to tumor necrosis factor / epidermal growth factor receptor signaling pathway
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.86 Å
AuthorsYin, J. / Jaiswal, B.S. / Wang, W.
CitationJournal: Clin. Cancer Res. / Year: 2018
Title: ERK Mutations and Amplification Confer Resistance to ERK-Inhibitor Therapy.
Authors: Jaiswal, B.S. / Durinck, S. / Stawiski, E.W. / Yin, J. / Wang, W. / Lin, E. / Moffat, J. / Martin, S.E. / Modrusan, Z. / Seshagiri, S.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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


Theoretical massNumber of molelcules
Total (without water)40,5341
Polymers40,5341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.870, 65.400, 116.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 40533.629 Da / Num. of mol.: 1 / Fragment: residues 13-360 / Mutation: G169D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 10% isopropanol, and 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.86→50 Å / Num. obs: 57377 / % possible obs: 92.3 % / Redundancy: 7.4 % / Net I/σ(I): 18.5
Reflection shellResolution: 2.86→2.87 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.86→50 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2719 645 4.55 %
Rwork0.2197 --
obs0.2218 14184 92.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 0 2757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022820
X-RAY DIFFRACTIONf_angle_d0.5173819
X-RAY DIFFRACTIONf_dihedral_angle_d11.1841073
X-RAY DIFFRACTIONf_chiral_restr0.022423
X-RAY DIFFRACTIONf_plane_restr0.003489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8603-3.08110.33881270.3082489X-RAY DIFFRACTION85
3.0811-3.39120.31731400.26482572X-RAY DIFFRACTION89
3.3912-3.88180.25391300.23882761X-RAY DIFFRACTION94
3.8818-4.89020.23311290.19322862X-RAY DIFFRACTION97
4.8902-57.07370.27721190.19072855X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82930.1973-0.12321.1720.60392.3720.02880.1702-0.3287-0.3864-0.2077-0.07860.6956-0.1261-0.29510.5478-0.05480.12640.23410.03970.299512.23433.96786.4777
22.66680.707-1.50742.2184-0.16523.11410.1797-0.0983-0.04240.0464-0.12420.0553-0.2522-0.16740.01070.0927-0.0282-0.03520.219-0.03690.2175.083916.436726.3089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 2:108
2X-RAY DIFFRACTION2(chain A and resi 109:360)

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