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- PDB-4iz5: Structure of the complex between ERK2 phosphomimetic mutant and PEA-15 -

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Basic information

Entry
Database: PDB / ID: 4iz5
TitleStructure of the complex between ERK2 phosphomimetic mutant and PEA-15
Components
  • Astrocytic phosphoprotein PEA-15
  • Mitogen-activated protein kinase 1
KeywordsTRANSFERASE / MAP Kinase / Death Effector Domain
Function / homology
Function and homology information


positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process ...positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated / negative regulation of glucose import / 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 / microtubule associated complex / 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 / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone mediated signaling pathway / carbohydrate transport / 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 / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / 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 / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / B cell receptor signaling pathway / Spry regulation of FGF signaling / peptidyl-threonine phosphorylation / Signaling by high-kinase activity BRAF mutants
Similarity search - Function
Astrocytic phosphoprotein PEA-15, death effector domain / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...Astrocytic phosphoprotein PEA-15, death effector domain / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Death-like domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / Mitogen-activated protein kinase 1 / Astrocytic phosphoprotein PEA-15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsMace, P.D. / Robinson, H. / Riedl, S.J.
CitationJournal: Nat Commun / Year: 2013
Title: Structure of ERK2 bound to PEA-15 reveals a mechanism for rapid release of activated MAPK.
Authors: Mace, P.D. / Wallez, Y. / Egger, M.F. / Dobaczewska, M.K. / Robinson, H. / Pasquale, E.B. / Riedl, S.J.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Mitogen-activated protein kinase 1
C: Mitogen-activated protein kinase 1
D: Mitogen-activated protein kinase 1
E: Astrocytic phosphoprotein PEA-15
F: Astrocytic phosphoprotein PEA-15
G: Astrocytic phosphoprotein PEA-15
H: Astrocytic phosphoprotein PEA-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,12428
Polymers225,8788
Non-polymers3,24620
Water0
1
A: Mitogen-activated protein kinase 1
G: Astrocytic phosphoprotein PEA-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2817
Polymers56,4702
Non-polymers8115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-80 kcal/mol
Surface area20310 Å2
MethodPISA
2
B: Mitogen-activated protein kinase 1
H: Astrocytic phosphoprotein PEA-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2817
Polymers56,4702
Non-polymers8115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-73 kcal/mol
Surface area19970 Å2
MethodPISA
3
C: Mitogen-activated protein kinase 1
F: Astrocytic phosphoprotein PEA-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2817
Polymers56,4702
Non-polymers8115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-81 kcal/mol
Surface area20320 Å2
MethodPISA
4
D: Mitogen-activated protein kinase 1
E: Astrocytic phosphoprotein PEA-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2817
Polymers56,4702
Non-polymers8115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-80 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.801, 149.129, 98.869
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.667906, 0.51488, -0.537401), (0.530014, -0.835977, -0.142219), (-0.522481, -0.189841, -0.831248)-10.92135, 28.61932, -7.94119
3given(-0.997086, -0.050848, 0.056866), (0.053678, -0.997336, 0.049398), (0.054203, 0.052306, 0.997159)-40.33215, 79.88192, -50.76248
4given(-0.66344, -0.582288, -0.469881), (-0.574483, 0.798767, -0.17872), (0.479392, 0.151369, -0.864448)30.36577, -51.08615, 42.16953

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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: 41126.227 Da / Num. of mol.: 4 / Fragment: unp residues 8-360 / Mutation: T185E
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) / Strain (production host): BL21(DE3)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Protein
Astrocytic phosphoprotein PEA-15 / 15 kDa phosphoprotein enriched in astrocytes / Phosphoprotein enriched in diabetes / PED


Mass: 15343.362 Da / Num. of mol.: 4 / Fragment: unp residues 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEA15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15121
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4

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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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris and 2.0 M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.19→29.8 Å / Num. obs: 36572 / % possible obs: 98.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0107refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→29.8 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.839 / SU B: 62.307 / SU ML: 0.483 / Cross valid method: THROUGHOUT / ESU R Free: 0.594 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29193 1930 5 %RANDOM
Rwork0.24274 ---
obs0.24515 36572 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.066 Å2
Baniso -1Baniso -2Baniso -3
1-6.87 Å20 Å2-0.85 Å2
2---6.18 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 3.19→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14061 0 188 0 14249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.98719752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5751711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74124.416702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.302152578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1351584
X-RAY DIFFRACTIONr_chiral_restr0.0760.22209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.19→3.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 117 -
Rwork0.306 2244 -
obs--83.31 %
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)
12.9804-1.8124-0.54823.38840.67751.8418-0.0411-0.1344-0.16530.03010.10860.1677-0.1584-0.1037-0.06760.0273-0.0167-0.00430.11460.07030.04741.4094.6728.69
21.62020.91520.17773.95460.25121.65990.21280.1628-0.0418-0.1088-0.01420.01970.15630.1277-0.19870.09530.0881-0.06390.180.00430.1191-13.10223.197-17.005
33.4409-1.5420.40052.89040.17522.55940.0320.09-0.00520.1597-0.23290.2560.0195-0.20.20090.1965-0.01830.00670.236-0.11430.0725-42.43775.98857.943
42.17750.3030.29896.2218-0.70041.53610.15530.1262-0.1708-0.4241-0.0753-0.1230.01-0.0541-0.08010.1590.04990.09970.1424-0.00490.1162-28.8956.32932.603
54.1369-0.52130.30979.14511.22895.223-0.1634-0.3477-0.38780.97130.2861-0.39060.03580.3187-0.12260.29080.0055-0.05940.25170.15850.2149-21.02940.71558.445
610.08760.1793-4.8058.8017-0.19857.03880.0212-0.03950.7709-0.09590.0714-0.5285-1.1246-0.0475-0.09260.51160.1195-0.09680.0462-0.03310.2393-36.59796.72635.329
710.7055-0.79715.30019.77773.57734.3430.4820.0886-0.4478-0.2863-0.37410.62250.3277-0.1185-0.10790.44980.0146-0.23620.16370.00590.2865-7-17.25-12.109
83.9731-1.4346-2.213710.2955-1.73334.7468-0.3358-0.17650.05150.72040.4490.20030.2558-0.2871-0.11330.09270.00580.02140.1761-0.05910.0516-18.70640.7458.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 357
2X-RAY DIFFRACTION1A900 - 904
3X-RAY DIFFRACTION2B11 - 357
4X-RAY DIFFRACTION2B900 - 904
5X-RAY DIFFRACTION3C11 - 357
6X-RAY DIFFRACTION3C900 - 904
7X-RAY DIFFRACTION4D11 - 357
8X-RAY DIFFRACTION4D900 - 904
9X-RAY DIFFRACTION5E1 - 86
10X-RAY DIFFRACTION6F1 - 86
11X-RAY DIFFRACTION7G1 - 86
12X-RAY DIFFRACTION8H1 - 86

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