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- PDB-3o71: Crystal structure of ERK2/DCC peptide complex -

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Basic information

Entry
Database: PDB / ID: 3o71
TitleCrystal structure of ERK2/DCC peptide complex
Components
  • Mitogen-activated protein kinase 1
  • Peptide of Deleted in Colorectal Cancer
KeywordsTRANSFERASE/PROTEIN BINDING / protein-peptide complex / Kinase / DCC / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation ...Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / growth cone membrane / Recycling pathway of L1 / neural crest cell development / diadenosine tetraphosphate biosynthetic process / corpus callosum development / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / optic nerve development / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / postsynaptic modulation of chemical synaptic transmission / : / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / axon development / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / progesterone receptor signaling pathway / androgen receptor signaling pathway / pseudopodium / negative regulation of cell differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / steroid hormone receptor signaling pathway / decidualization / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / axonal growth cone / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / sensory perception of pain / positive regulation of telomere maintenance via telomerase / response to amphetamine
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / Mitogen-activated protein (MAP) kinase, ERK1/2 / Immunoglobulin domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...Neogenin, C-terminal / Neogenin C-terminus / Mitogen-activated protein (MAP) kinase, ERK1/2 / Immunoglobulin domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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
THIOCYANATE ION / Mitogen-activated protein kinase 1 / Netrin receptor DCC
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMa, W.F. / Shang, Y. / Wei, Z.Y. / Wen, W.Y. / Wang, W.N. / Zhang, M.J.
CitationJournal: Structure / Year: 2010
Title: Phosphorylation of DCC by ERK2 is facilitated by direct docking of the receptor P1 domain to the kinase
Authors: Ma, W. / Shang, Y. / Wei, Z. / Wen, W. / Wang, W. / Zhang, M.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Peptide of Deleted in Colorectal Cancer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8014
Polymers44,6842
Non-polymers1162
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.178, 87.178, 94.459
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21A-521-

HOH

31A-532-

HOH

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Components

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / Extracellular signal-regulated kinase 2 / ERK-2 / Mitogen-activated protein ...MAP kinase 1 / MAPK 1 / Extracellular signal-regulated kinase 2 / ERK-2 / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2 / MAP kinase isoform p42 / p42-MAPK / ERT1


Mass: 41330.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Production host: Escherichia coli (E. coli)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Protein/peptide Peptide of Deleted in Colorectal Cancer / Deleted in colorectal carcinoma / isoform CRA_a


Mass: 3353.870 Da / Num. of mol.: 1 / Fragment: UNP residues 1140-1166 / Source method: obtained synthetically / Details: This sequence occurs naturally in rats / References: UniProt: Q63155
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1 M HEPES, pH 6.9, 18% PEG3350, and 0.12 M KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 30642 / Num. obs: 30642 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.59 / Num. unique all: 1538 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.144 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1547 5 %RANDOM
Rwork0.19894 ---
all0.20097 29094 --
obs0.20097 29094 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 6 176 3005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222918
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9753955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7795352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.723.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37315519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3181520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212201
X-RAY DIFFRACTIONr_mcbond_it1.19421759
X-RAY DIFFRACTIONr_mcangle_it2.08132850
X-RAY DIFFRACTIONr_scbond_it3.06841159
X-RAY DIFFRACTIONr_scangle_it4.81961101
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 114 -
Rwork0.272 2137 -
obs--99.82 %
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)
126.5904-42.173214.120552.4541-18.95585.13990.59581.4641-0.3239-1.9486-0.64341.54060.64510.11080.04761.3151-0.6873-0.05511.8123-0.33970.3934-38.0724.2125.302
289.9946-7.350421.39581.997-3.039717.98931.19260.1927-2.9321-0.8625-0.29730.08851.3735-0.374-0.89530.8627-0.05320.2150.5648-0.01680.5121-17.518-16.0978.819
33.1472-2.5278-0.1155.10964.35725.4785-0.11930.04540.5889-0.3774-0.03960.22640.11590.34660.15890.86440.0771-0.25080.4427-0.06850.4844-28.9262.4737.7
48.75970.0892-2.08843.9081-1.97981.4584-0.10470.432-0.1849-0.07020.1020.13670.0679-0.19770.00280.1483-0.02980.00250.1471-0.05320.044-36.3655.40524.481
51.09490.3869-0.22232.99141.30934.2751-0.02070.03340.023-0.0512-0.0371-0.13570.12060.03570.05780.0212-0.02210.02820.0575-0.03360.1321-24.295-17.37230.251
60.574-0.0512-0.25011.3608-0.25121.0067-0.0192-0.1041-0.01980.14-0.0251-0.2660.02060.07130.04430.0328-0.0166-0.02510.0877-0.03670.1293-23.789-18.17137.596
70.6485-0.6676-0.27882.6708-0.26260.97850.00770.18380.0127-0.289-0.054-0.2099-0.0382-0.04190.04630.0629-0.04590.03060.1215-0.02740.0827-23.708-3.86721.838
82.135-1.7042-0.88554.16671.46381.33030.0629-0.08210.09290.0133-0.03160.0094-0.195-0.2368-0.03130.08630.00810.03070.1397-0.01280.0999-35.162-11.37436.399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 19
2X-RAY DIFFRACTION2B1148 - 1155
3X-RAY DIFFRACTION3A20 - 50
4X-RAY DIFFRACTION4A51 - 71
5X-RAY DIFFRACTION5A204 - 223
6X-RAY DIFFRACTION6A224 - 335
7X-RAY DIFFRACTION7A72 - 174
8X-RAY DIFFRACTION8A180 - 200

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