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- PDB-4h3p: Crystal structure of human ERK2 complexed with a MAPK docking peptide -

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Basic information

Entry
Database: PDB / ID: 4h3p
TitleCrystal structure of human ERK2 complexed with a MAPK docking peptide
Components
  • Mitogen-activated protein kinase 1
  • Ribosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / kinase domain / signaling / linear motif / surface mutation
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of hepatic stellate cell activation / hepatocyte proliferation / CREB phosphorylation / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / TORC1 signaling ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of hepatic stellate cell activation / hepatocyte proliferation / CREB phosphorylation / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / TORC1 signaling / 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 / positive regulation of macrophage proliferation / regulation of cellular pH / negative regulation of TOR signaling / 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 / protein serine/threonine/tyrosine kinase activity / 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 / positive regulation of cell differentiation / 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
Similarity search - Function
Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Mitogen-activated protein (MAP) kinase, ERK1/2 / Extension to Ser/Thr-type protein kinases / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / AGC-kinase, C-terminal ...Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Mitogen-activated protein (MAP) kinase, ERK1/2 / Extension to Ser/Thr-type protein kinases / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGogl, G. / Toeroe, I. / Remenyi, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Protein-peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase
Authors: Gogl, G. / Toeroe, I. / Remenyi, A.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,2306
Polymers88,2184
Non-polymers1,0122
Water3,189177
1
A: Mitogen-activated protein kinase 1
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6153
Polymers44,1092
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-4 kcal/mol
Surface area16410 Å2
MethodPISA
2
D: Mitogen-activated protein kinase 1
E: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6153
Polymers44,1092
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-8 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.480, 58.770, 79.180
Angle α, β, γ (deg.)100.93, 98.96, 90.01
Int Tables number1
Space group name H-MP1

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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.: 2 / Fragment: kinase domain / Mutation: R77A, E314A
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
#2: Protein/peptide Ribosomal protein S6 kinase alpha-1 / 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: 2664.217 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOCKING PEPTIDE, UNP residues 712-735 / Mutation: S719A, Q724A / Source method: obtained synthetically / Details: Synthetic construct / 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.: 2 / 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.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-30% PEG6000, 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: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 2M / Detector: PIXEL / Date: Jul 31, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.37 Å / Num. all: 32220 / Num. obs: 30568 / % possible obs: 94.9 % / Observed criterion σ(F): 2.39 / Observed criterion σ(I): 2.39
Reflection shellResolution: 2.3→2.382 Å / % possible all: 93.31

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TEI

3tei


Resolution: 2.3→42.37 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1542 5.05 %RANDOM
Rwork0.178 ---
obs0.1804 30560 94.92 %-
all-30560 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 62 177 5926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095884
X-RAY DIFFRACTIONf_angle_d1.3547992
X-RAY DIFFRACTIONf_dihedral_angle_d20.5082252
X-RAY DIFFRACTIONf_chiral_restr0.089889
X-RAY DIFFRACTIONf_plane_restr0.0071013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.37450.31471290.2412257893
2.3745-2.45930.25721320.2286262193
2.4593-2.55780.32631530.2287263195
2.5578-2.67420.25981390.2125267896
2.6742-2.81520.29481330.2123265795
2.8152-2.99150.28221450.2025266796
2.9915-3.22240.26021160.184269196
3.2224-3.54650.21571290.1662266795
3.5465-4.05940.18381440.1489266996
4.0594-5.1130.19031630.143257394
5.113-42.37790.18581590.1766258694
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)
12.108-0.8001-0.33492.36110.31041.16670.0138-0.2403-0.00780.15210-0.6867-0.11880.23780.04390.1629-0.0058-0.02310.21860.01780.3798-1.7617-7.82432.4409
25.12394.83623.95015.67163.86943.8069-0.30780.54840.7659-0.25220.2210.0705-0.47360.23380.04320.2112-0.0281-0.02270.16470.02330.3309-13.71536.0521-1.1505
30.822-0.26360.14741.8378-1.68222.9211-0.07010.0688-0.192-0.4048-0.0415-0.0490.28390.0020.07870.214-0.0133-0.00490.1781-0.02910.3245-10.2751-1.9945-12.2788
44.1504-1.6039-2.84731.06551.15981.6283-0.1241-1.002-0.18450.31250.28970.182-0.29660.2806-0.10360.4478-0.0067-0.01410.36020.05780.355-9.923417.2931-15.8351
53.39221.762-0.114.2322-1.92313.3551-0.14780.29760.65060.0403-0.04210.1185-0.67010.03060.17610.4691-0.0002-0.07350.31570.0150.2939-5.429819.0222-26.1467
60.7712-0.23570.27691.3422-1.02083.06270.00080.1631-0.0934-0.31880.05530.24980.2246-0.4531-0.0730.2444-0.0513-0.06650.2857-0.03210.3311-16.3984.2116-16.8234
72.0810.7443-0.08712.58230.22190.341-0.00270.1129-0.0121-0.03590.0269-0.43260.10020.1327-0.00880.16290.0062-0.02180.20980.02160.2839-25.533933.9139-0.3747
80.6527-0.0572-0.17971.7553-2.08043.0996-0.125-0.04880.09960.38530.0111-0.1894-0.29760.03480.06720.18670.0052-0.03590.2095-0.01690.2592-30.84331.860113.4705
92.80670.67473.0320.8120.8753.3667-0.11120.59230.1077-0.54960.13040.11150.7527-0.34510.00870.4323-0.0869-0.00090.40820.00620.3309-31.180612.31418.7036
102.3253-1.3719-0.33952.005-1.23223.0863-0.03270.3140.07150.5203-0.039-0.0191-0.14960.33610.0690.3134-0.0208-0.00680.22030.02540.1906-29.440622.667225.1097
111.5425-1.1658-1.58276.5794-0.28933.1483-0.1228-0.1642-0.54020.21960.1371-0.67610.48980.2821-0.01380.24580.01520.04340.3060.0580.3393-20.275512.542324.7031
122.0023-2.7198-9.36272.015-4.38492.0071-0.12430.3481-1.0864-0.5465-0.00691.16010.5261-2.0650.23940.7374-0.1797-0.14940.73780.12160.8936-33.94874.167433.6453
135.08471.87983.32970.73360.96514.2248-0.0722-0.1220.3149-0.9384-0.29580.8770.5345-0.72760.22761.18810.0171-0.13880.64340.09361.502-31.6933-1.181724.688
142.6078-0.45840.6634.17440.07851.6349-0.2382-0.1296-0.14611.43480.19880.0080.35020.55230.00660.69350.0624-0.06540.41960.06960.2541-24.897518.672537.2449
152.3096-0.96880.97082.73990.10151.6992-0.0078-0.348-0.03120.86270.05860.416-0.4971-0.5065-0.03960.46620.03730.12120.42190.02290.2711-39.166727.296629.69
164.0147-0.9092-3.15526.68135.43412.0526-0.359-0.2689-0.6204-0.05220.16530.83320.4135-0.68330.41290.42060.0263-0.01870.50420.07440.6957-43.256619.53613.4237
173.81-0.1129-0.53617.68490.75034.06640.19610.3984-0.2265-0.8354-0.30441.42010.1313-0.74970.07060.246-0.0065-0.11620.2767-0.02920.3687-38.575728.9932-7.5893
182.5192-0.7973-1.57325.50233.17226.18990.3396-0.78970.14490.1222-0.0461-0.06240.22770.4273-0.14030.85540.13740.21360.6395-0.04820.8767-2.7584-14.4968-24.6985
192.00741.4033-7.27246.29882.74797.5502-0.05721.0212-0.6237-1.10470.28390.23920.87010.1941-0.16591.03440.30110.04530.6316-0.09030.4408-16.4968-15.0915-24.6392
209.57551.64062.44988.8529-7.62722.0015-0.0434-0.1579-0.16210.70910.5351-0.49110.1340.9406-0.46931.017-0.26930.03820.917-0.33340.7189-19.642943.432623.1349
214.19943.37852.93494.80580.21324.2917-0.0033-0.43710.72750.8876-0.3106-0.0782-0.7002-0.23090.27921.1978-0.10760.02060.5094-0.11090.8786-33.925545.352627.0204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 11 through 61 )
2X-RAY DIFFRACTION2chain A and (resid 62 through 77 )
3X-RAY DIFFRACTION3chain A and (resid 78 through 177 )
4X-RAY DIFFRACTION4chain A and (resid 178 through 207 )
5X-RAY DIFFRACTION5chain A and (resid 208 through 275 )
6X-RAY DIFFRACTION6chain A and (resid 276 through 359 )
7X-RAY DIFFRACTION7chain D and (resid 11 through 77 )
8X-RAY DIFFRACTION8chain D and (resid 78 through 177 )
9X-RAY DIFFRACTION9chain D and (resid 178 through 206 )
10X-RAY DIFFRACTION10chain D and (resid 207 through 223 )
11X-RAY DIFFRACTION11chain D and (resid 224 through 244 )
12X-RAY DIFFRACTION12chain D and (resid 245 through 254 )
13X-RAY DIFFRACTION13chain D and (resid 255 through 266 )
14X-RAY DIFFRACTION14chain D and (resid 267 through 293 )
15X-RAY DIFFRACTION15chain D and (resid 294 through 326 )
16X-RAY DIFFRACTION16chain D and (resid 327 through 339 )
17X-RAY DIFFRACTION17chain D and (resid 340 through 359 )
18X-RAY DIFFRACTION18chain B and (resid 712 through 720 )
19X-RAY DIFFRACTION19chain B and (resid 721 through 727 )
20X-RAY DIFFRACTION20chain E and (resid 712 through 716 )
21X-RAY DIFFRACTION21chain E and (resid 717 through 728 )

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