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- PDB-3sa0: Complex of ERK2 with norathyriol -

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Basic information

Entry
Database: PDB / ID: 3sa0
TitleComplex of ERK2 with norathyriol
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / norathyriol complex / signal-regulated kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / 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 / cytosine metabolic process / ERKs are inactivated ...phospho-PLA2 pathway / Signaling by MAPK mutants / 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 / cytosine metabolic process / 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 / outer ear morphogenesis / Regulation of the apoptosome activity / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / 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 / ERK/MAPK targets / androgen receptor signaling pathway / pseudopodium / RUNX2 regulates osteoblast differentiation / Recycling pathway of L1 / progesterone receptor signaling pathway / MAPK1 (ERK2) activation / negative regulation of cell differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone mediated signaling pathway / 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 / Nuclear events stimulated by ALK signaling in cancer / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / stress-activated MAPK cascade / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / cellular response to amino acid starvation / myelination / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / Signal transduction by L1 / caveola / long-term synaptic potentiation / 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 / B cell receptor signaling pathway / peptidyl-threonine phosphorylation / Spry regulation of FGF signaling / response to nicotine / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / Oncogene Induced Senescence / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation
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
norathyriol / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5947 Å
AuthorsKurinov, I. / Malakhova, M.
CitationJournal: Cancer Res. / Year: 2012
Title: Norathyriol Suppresses Skin Cancers Induced by Solar Ultraviolet Radiation by Targeting ERK Kinases.
Authors: Li, J. / Malakhova, M. / Mottamal, M. / Reddy, K. / Kurinov, I. / Carper, A. / Langfald, A. / Oi, N. / Kim, M.O. / Zhu, F. / Sosa, C.P. / Zhou, K. / Bode, A.M. / Dong, Z.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,0293
Polymers41,6731
Non-polymers3562
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.687, 69.411, 59.721
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: 41673.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERK2, MAPK1, PRKM1, PRKM2 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL
References: UniProt: P28482, mitogen-activated protein kinase
#2: Chemical ChemComp-NRA / norathyriol / 1,3,6,7-tetrahydroxy-9H-xanthen-9-one


Mass: 260.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8O6
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Precipitant: 1.1 M - 1.3 M ammonium sulfate, 2% PEG 500 MME, 0.1 M Hepes, pH 7.5. The protein was in 80-120 mM Nacl, Tris 15 mM, pH 8.0, 10-20 mM b-ME Protein was mixed with precipitant at 1: ...Details: Precipitant: 1.1 M - 1.3 M ammonium sulfate, 2% PEG 500 MME, 0.1 M Hepes, pH 7.5. The protein was in 80-120 mM Nacl, Tris 15 mM, pH 8.0, 10-20 mM b-ME Protein was mixed with precipitant at 1:1 ratio, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9795
SYNCHROTRONAPS 24-ID-C20.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2009 / Details: HF and VF mirrors
RadiationMonochromator: double-crystals monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5947→30 Å / Num. all: 49935 / Num. obs: 49914 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.4
Reflection shellResolution: 1.5947→1.66 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVO

1tvo


Resolution: 1.5947→29.568 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1997 4 %5%
Rwork0.1642 ---
obs0.1656 49907 99.56 %-
all-49914 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.785 Å2 / ksol: 0.439 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6563 Å20 Å2-0.2172 Å2
2--2.2609 Å20 Å2
3---1.3953 Å2
Refinement stepCycle: LAST / Resolution: 1.5947→29.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 24 296 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143029
X-RAY DIFFRACTIONf_angle_d1.4594114
X-RAY DIFFRACTIONf_dihedral_angle_d14.3111149
X-RAY DIFFRACTIONf_chiral_restr0.083446
X-RAY DIFFRACTIONf_plane_restr0.008527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5947-1.63460.28111410.2223254X-RAY DIFFRACTION95
1.6346-1.67880.28071320.21193443X-RAY DIFFRACTION100
1.6788-1.72820.24551410.19693425X-RAY DIFFRACTION100
1.7282-1.7840.20771470.17783371X-RAY DIFFRACTION100
1.784-1.84770.19851460.16113442X-RAY DIFFRACTION100
1.8477-1.92170.17831350.15333445X-RAY DIFFRACTION100
1.9217-2.00910.19861490.14863397X-RAY DIFFRACTION100
2.0091-2.1150.18471540.15253432X-RAY DIFFRACTION100
2.115-2.24750.18531310.14943425X-RAY DIFFRACTION100
2.2475-2.42090.18181440.15223453X-RAY DIFFRACTION100
2.4209-2.66440.19861520.15343418X-RAY DIFFRACTION100
2.6644-3.04960.18711410.16533473X-RAY DIFFRACTION100
3.0496-3.84090.19131390.16313456X-RAY DIFFRACTION100
3.8409-29.5730.21331450.17133476X-RAY DIFFRACTION99
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)
11.5722-0.4804-0.33160.4521-0.35312.62840.03920.11270.5350.09760.15790.0366-0.6393-0.5935-0.04540.30780.063-0.00040.36820.07530.2032-13.801612.474831.7206
22.11440.82660.30240.7960.08621.03960.03560.03070.1649-0.0109-0.0073-0.0158-0.0170.0388-0.02880.11030.02940.01380.07980.00620.13020.01356.703155.8008
31.9812-0.74822.24631.2564-0.94724.62290.31930.5351-0.4496-0.18410.0594-0.35110.25120.4101-0.33980.32990.0356-0.00940.3453-0.00620.193-5.39425.407721.9543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:109)
2X-RAY DIFFRACTION2(chain A and resid 110:336 )
3X-RAY DIFFRACTION3(chain A and resid 337:360)

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