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- PDB-2y9q: Crystal structure of human ERK2 complexed with a MAPK docking peptide -

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Basic information

Entry
Database: PDB / ID: 2y9q
TitleCrystal structure of human ERK2 complexed with a MAPK docking peptide
Components
  • MAP KINASE-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1
  • MITOGEN-ACTIVATED PROTEIN KINASE 1
KeywordsTRANSFERASE / SIGNALING / PROTEIN-PROTEIN INTERACTION
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / 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 / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process ...calcium-dependent protein serine/threonine kinase activity / 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 / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / Signaling by MAP2K mutants / Signaling by NODAL / ERKs are inactivated / response to epidermal growth factor / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / calcium/calmodulin-dependent protein kinase activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / labyrinthine layer blood vessel development / ERBB signaling pathway / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / positive regulation of peptidyl-threonine phosphorylation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / MAPK1 (ERK2) activation / positive regulation of macrophage chemotaxis / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / face development / lung morphogenesis / positive regulation of telomere maintenance / Recycling pathway of L1 / pseudopodium / Bergmann glial cell differentiation / androgen receptor signaling pathway / thyroid gland development / steroid hormone receptor signaling pathway / Advanced glycosylation endproduct receptor signaling / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / negative regulation of cell differentiation / regulation of ossification / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate WASPs and WAVEs / JUN kinase activity / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / phosphatase binding / Schwann cell development / Growth hormone receptor signaling / progesterone receptor signaling pathway / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / ERK1 and ERK2 cascade / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ESR-mediated signaling / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to nicotine / 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 / positive regulation of cholesterol biosynthetic process / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / Oncogene Induced Senescence / caveola
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 ...: / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 1 / MAP kinase-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBarkai, T. / Garai, A. / Toeroe, I. / 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
DepositionFeb 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: MAP KINASE-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1393
Polymers43,6332
Non-polymers5061
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-11.9 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.360, 65.880, 95.050
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 / ERK2


Mass: 41588.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) / Variant (production host): PLYSS
References: UniProt: P28482, mitogen-activated protein kinase
#2: Protein/peptide MAP KINASE-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1 / MAP KINASE SIGNAL-INTEGRATING KINASE 1 / MNK1


Mass: 2044.516 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOCKING PEPTIDE, RESIDUES 434-451 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: Q9BUB5, 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


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, CYS 440 TO SER

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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: 2.35 Å3/Da / Density % sol: 47.75 % / Description: NONE
Crystal growpH: 6.5 / Details: 12% PEG 20000, 100 MM MIB BUFFER PH 6.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 25, 2010 / Details: DUAL SLITS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→53.86 Å / Num. obs: 59403 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.32 % / Biso Wilson estimate: 14.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.82
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.92 / % possible all: 91.4

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Processing

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

2gph


Resolution: 1.55→53.856 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.38 / Stereochemistry target values: ML
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS FOR REFINEMENT. RESIDUES FROM A-1 TO A8, A359, A360, AND B454 ARE DISORDERED. RESIDUES A79, A180, AND A314 ARE MODELLED WITH TRUNCATED SIDECHAINS.
RfactorNum. reflection% reflection
Rfree0.1768 2000 3.4 %
Rwork0.155 --
obs0.1557 59398 98.54 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.593 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.3715 Å20 Å20 Å2
2--3.7345 Å20 Å2
3----2.363 Å2
Refinement stepCycle: LAST / Resolution: 1.55→53.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 31 546 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093174
X-RAY DIFFRACTIONf_angle_d1.3274325
X-RAY DIFFRACTIONf_dihedral_angle_d15.7451264
X-RAY DIFFRACTIONf_chiral_restr0.072476
X-RAY DIFFRACTIONf_plane_restr0.006551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58870.30241250.28413575X-RAY DIFFRACTION87
1.5887-1.63170.24921370.24673932X-RAY DIFFRACTION96
1.6317-1.67970.26661420.21664107X-RAY DIFFRACTION99
1.6797-1.73390.21341440.19784097X-RAY DIFFRACTION100
1.7339-1.79590.22781430.17964108X-RAY DIFFRACTION100
1.7959-1.86780.19131430.16714112X-RAY DIFFRACTION100
1.8678-1.95280.17971440.15714119X-RAY DIFFRACTION100
1.9528-2.05580.19191430.15024138X-RAY DIFFRACTION100
2.0558-2.18460.16311450.14214153X-RAY DIFFRACTION100
2.1846-2.35330.19671450.13614148X-RAY DIFFRACTION100
2.3533-2.59010.16171440.13694157X-RAY DIFFRACTION100
2.5901-2.96480.15761470.1384214X-RAY DIFFRACTION100
2.9648-3.73530.16461470.13934198X-RAY DIFFRACTION100
3.7353-53.88840.14281510.14864340X-RAY DIFFRACTION98
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)
10.55240.0871-0.45984.1363-0.2321.34960.03290.03270.0869-0.2112-0.03790.3127-0.0777-0.23960.01280.11980.0122-0.0190.1617-0.04210.142345.325138.241417.5988
22.99520.4585-2.07971.1251-0.17931.9397-0.0747-0.1273-0.07890.0509-0.01030.02780.14650.06010.08410.12890.0108-0.01740.1244-0.00920.081953.762727.047621.1669
31.384-0.0246-0.43460.66290.26061.61190.0041-0.00840.02350.0091-0.0152-0.00560.0035-0.009-0.0180.08190.0011-0.01140.0743-0.01070.090361.610930.45396.2188
43.05950.7012-0.32431.74150.57351.1569-0.04540.004-0.26110.0424-0.00440.07010.1547-0.08630.03860.09520.0030.00680.1027-0.0110.11157.191718.0716-3.1052
53.80852.7558-2.30732.4025-1.4351.7886-0.1542-0.0219-0.65670.0404-0.0189-0.3370.21620.04620.18190.25590.02070.04220.2038-0.04890.274761.63695.4742-10.7947
65.6583-0.45141.31454.5265-2.79346.56250.03330.40830.0274-0.2944-0.0173-0.03380.1220.2436-0.03270.10150.0090.01660.1089-0.01980.098670.272226.5331-12.7964
71.25610.1555-0.60070.94820.26480.6766-0.0313-0.1105-0.11150.1501-0.0063-0.03630.08870.12850.04560.12110.0249-0.01920.12050.00580.131770.922.10117.4598
84.4142.39480.87237.34881.60793.28320.0746-0.3515-0.05010.6450.0201-0.21870.21950.1189-0.09520.15940.0304-0.00850.1862-0.02170.084851.595724.936729.4367
96.7856-1.61283.58523.7439-0.95414.3227-0.29390.01640.97550.1472-0.064-0.2454-0.47110.00780.32650.2487-0.0330.00950.1088-0.0110.247871.304744.73563.7291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 9:61
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 62:100
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 101:180
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 181:244
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 245:274
6X-RAY DIFFRACTION6CHAIN A AND RESSEQ 275:293
7X-RAY DIFFRACTION7CHAIN A AND RESSEQ 294:339
8X-RAY DIFFRACTION8CHAIN A AND RESSEQ 340:358
9X-RAY DIFFRACTION9CHAIN B

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