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- PDB-3tei: Crystal structure of human ERK2 complexed with a MAPK docking peptide -

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Basic information

Entry
Database: PDB / ID: 3tei
TitleCrystal structure of human ERK2 complexed with a MAPK docking peptide
Components
  • Mitogen-activated protein kinase 1
  • Ribosomal protein S6 kinase alpha-1Ribosome
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / negative regulation of TOR signaling / 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 cytoskeleton organization / 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 / response to exogenous dsRNA / lung morphogenesis / ERBB2-ERBB3 signaling pathway / face development / Recycling pathway of L1 / Activation of the AP-1 family of transcription factors / androgen receptor signaling pathway / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / pseudopodium / progesterone receptor signaling pathway / positive regulation of telomere capping / MAPK1 (ERK2) activation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of cell differentiation / Bergmann glial cell differentiation / 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 / RHO GTPases Activate WASPs and WAVEs / regulation of ossification / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / stress-activated MAPK cascade / Schwann cell development / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / ERK1 and ERK2 cascade / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / myelination / NPAS4 regulates expression of target genes / protein serine/threonine/tyrosine kinase activity / 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 / response to nicotine / Regulation of PTEN gene transcription / Signal transduction by L1 / long-term synaptic potentiation / caveola / Negative regulation of FGFR3 signaling / positive regulation of cell differentiation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling
Similarity search - Function
Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein kinase, C-terminal / Protein kinase C terminal domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein kinase, C-terminal / Protein kinase C terminal domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 1 / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: Sci.Signal. / Year: 2012
Title: Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove.
Authors: Garai, A. / Zeke, A. / Gogl, G. / Toro, I. / Fordos, F. / Blankenburg, H. / Barkai, T. / Varga, J. / Alexa, A. / Emig, D. / Albrecht, M. / Remenyi, A.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6883
Polymers44,1822
Non-polymers5061
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.700, 58.980, 155.730
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 / 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: 41444.633 Da / Num. of mol.: 1 / Mutation: R77A, E314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Protein/peptide Ribosomal protein S6 kinase alpha-1 / Ribosome / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase- ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPK-activated protein kinase 1a / MAPKAP kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 2737.268 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOCKING PEPTIDE, RESIDUES 712-735 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 296 K / pH: 6.5
Details: 27-29% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.1 Å / Num. obs: 15190 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 12.49 %
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 12.41 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.97 / Num. unique all: 1113 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_713)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GPH

2gph


Resolution: 2.404→47.015 Å / SU ML: 0.69 / σ(F): 1.35 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 749 4.94 %
Rwork0.1969 --
obs0.1988 15164 96.99 %
all-11831 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.103 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8123 Å2-0 Å20 Å2
2---9.8632 Å20 Å2
3---11.6755 Å2
Refinement stepCycle: LAST / Resolution: 2.404→47.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 31 115 3004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052957
X-RAY DIFFRACTIONf_angle_d1.1714015
X-RAY DIFFRACTIONf_dihedral_angle_d19.1591140
X-RAY DIFFRACTIONf_chiral_restr0.089449
X-RAY DIFFRACTIONf_plane_restr0.007508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4041-2.58970.29081400.25532879X-RAY DIFFRACTION99
2.5897-2.85020.29991540.24952859X-RAY DIFFRACTION98
2.8502-3.26260.27551550.2192883X-RAY DIFFRACTION98
3.2626-4.11020.20771670.17682842X-RAY DIFFRACTION96
4.1102-47.0240.21061330.17842952X-RAY DIFFRACTION93
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)
15.938-0.04562.23994.06460.01213.04540.27080.3187-0.5084-0.659-0.1801-0.8770.56770.23840.07470.2233-0.00010.08630.29740.06950.55950.90177.4696-3.5894
21.4699-0.10490.75193.1463-2.16023.6499-0.007-0.06160.11810.336-0.0052-0.16420.1381-0.05350.01910.12870.0180.0270.2387-0.00280.3136-8.63833.0649.2648
36.6101-1.90290.93533.7521-2.82373.99010.10880.3435-0.32260.2522-0.0543-0.09330.7244-0.088-0.07580.4713-0.0050.01260.2693-0.01410.1524-6.0778-13.716821.0262
45.4854-3.9357-2.53074.17810.15644.9726-0.5182-0.2987-1.32410.2124-0.10970.59280.9237-0.00110.68421.2078-0.0296-0.00360.43950.07420.6121-8.2633-25.539230.638
53.434-0.6816-0.41324.3633-1.31892.5391-0.1959-0.9964-0.00321.5040.5417-0.1294-0.2557-0.6887-0.13780.88710.17710.0920.6267-0.02360.2346-11.3127-4.586233.184
61.7737-0.3496-1.26571.982-0.21545.2698-0.12750.0291-0.615-0.08760.50411.11470.7208-1.25680.15040.1994-0.08860.00140.51130.04470.7708-20.4873-2.51080.8913
70.7334-0.9793-1.33491.66962.24043.1465-0.3221-0.49810.0820.44940.15860.0518-0.91570.22420.01751.14990.168-0.0630.5463-0.13560.7066-7.910515.724225.5842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 10:37)
2X-RAY DIFFRACTION2chain 'A' and (resseq 38:170)
3X-RAY DIFFRACTION3chain 'A' and (resseq 171:244)
4X-RAY DIFFRACTION4chain 'A' and (resseq 245:275)
5X-RAY DIFFRACTION5chain 'A' and (resseq 276:318)
6X-RAY DIFFRACTION6chain 'A' and (resseq 319:358)
7X-RAY DIFFRACTION7chain 'B'

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