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- PDB-4h3q: Crystal structure of human ERK2 complexed with a MAPK docking peptide -

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Basic information

Entry
Database: PDB / ID: 4h3q
TitleCrystal structure of human ERK2 complexed with a MAPK docking peptide
Components
  • Dual specificity mitogen-activated protein kinase kinase 2
  • Mitogen-activated protein kinase 1
KeywordsTRANSFERASE / kinase domain / signaling / linear motif / surface mutation
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / JUN kinase kinase activity / regulation of axon regeneration / mitogen-activated protein kinase kinase / phospho-PLA2 pathway / MAP-kinase scaffold activity / Signaling by MAPK mutants / peptidyl-serine autophosphorylation / RAF-independent MAPK1/3 activation / Suppression of apoptosis ...epithelial cell proliferation involved in lung morphogenesis / JUN kinase kinase activity / regulation of axon regeneration / mitogen-activated protein kinase kinase / phospho-PLA2 pathway / MAP-kinase scaffold activity / Signaling by MAPK mutants / peptidyl-serine autophosphorylation / 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 / positive regulation of axonogenesis / 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 / peroxisomal membrane / 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 / positive regulation of cell motility / 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 / MAP kinase kinase activity / Recycling pathway of L1 / pseudopodium / Bergmann glial cell differentiation / Uptake and function of anthrax toxins / 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 / positive regulation of protein serine/threonine kinase activity / 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 / protein serine/threonine kinase activator activity / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / PDZ domain binding / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to nicotine
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 / Dual specificity mitogen-activated protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
B: Dual specificity mitogen-activated protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3563
Polymers42,8502
Non-polymers5061
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.750, 58.530, 159.150
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: 41372.461 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: R77A, E314A, I255G, C162S
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 Dual specificity mitogen-activated protein kinase kinase 2 / MAP kinase kinase 2 / MAPKK 2 / ERK activator kinase 2 / MAPK/ERK kinase 2 / MEK 2


Mass: 1477.816 Da / Num. of mol.: 1 / Fragment: DOCKING PEPTIDE, UNP residues 4-16 / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) Homo sapiens (human)
References: UniProt: P36507, mitogen-activated protein kinase 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.: 84 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG1500, 0.1M MIB, pH 5.5, 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: 2.2→47.15 Å / Num. all: 20638 / Num. obs: 20375 / % possible obs: 99.03 % / Observed criterion σ(F): 2.25 / Observed criterion σ(I): 2.25
Reflection shellResolution: 2.2→2.279 Å / % possible all: 96.49

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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: 2.2→47.149 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1047 5.14 %RANDOM
Rwork0.1813 ---
obs0.1839 20371 99.01 %-
all-20371 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 31 84 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013006
X-RAY DIFFRACTIONf_angle_d1.4154092
X-RAY DIFFRACTIONf_dihedral_angle_d19.0321141
X-RAY DIFFRACTIONf_chiral_restr0.098456
X-RAY DIFFRACTIONf_plane_restr0.006521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.31630.29741470.2602266798
2.3163-2.46140.27061290.22912754100
2.4614-2.65140.31091580.22312719100
2.6514-2.91820.26451520.20832743100
2.9182-3.34040.24741480.1919274599
3.3404-4.20820.21181740.1561280099
4.2082-47.16020.19491390.1613289698
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)
14.52992.47411.12814.13870.8592.52110.11660.32090.0115-0.1286-0.2006-0.88310.25620.22430.07690.18330.03950.04960.2960.05330.452-0.68628.1631-1.9044
22.0031-0.15721.93192.8918-1.2156.16440.0102-0.30260.160.40090.0520.12980.2655-0.3539-0.05980.1866-00.0530.2703-0.01280.2759-9.59090.833711.6344
35.6027-1.06831.04245.3976-1.86633.86680.2175-0.5543-0.72670.45020.26080.33021.1415-0.5184-0.46990.8963-0.0731-0.06760.55780.07690.318-6.1372-14.175826.9951
41.55950.0615-0.45062.70010.09246.9088-0.1884-0.4844-0.02980.19170.41570.59620.4633-0.9136-0.15070.23920.04450.02050.55440.02540.4787-19.1072-1.40354.6269
53.54931.02423.06115.8359-0.60493.53950.396-0.33250.2170.6312-0.40690.9011-1.262-0.6933-0.08281.06720.17080.01050.5946-0.12431.0291-5.4515.624925.025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 9:61)
2X-RAY DIFFRACTION2chain A and (resseq 62:180)
3X-RAY DIFFRACTION3chain A and (resseq 181:313)
4X-RAY DIFFRACTION4chain A and (resseq 314:360)
5X-RAY DIFFRACTION5chain B and (resseq 4:15)

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