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- PDB-3zu7: Crystal structure of a designed selected Ankyrin Repeat protein i... -
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Basic information
Entry | Database: PDB / ID: 3zu7 | ||||||
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Title | Crystal structure of a designed selected Ankyrin Repeat protein in complex with the MAP kinase ERK2 | ||||||
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![]() | TRANSFERASE/DE NOVO PROTEIN / TRANSFERASE-DE NOVO PROTEIN COMPLEX / TRANSFERASE / SELECTED BINDER / PROTEIN DESIGN | ||||||
Function / homology | ![]() 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 ...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 / Recycling pathway of L1 / neural crest cell development / diadenosine tetraphosphate biosynthetic process / 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 / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / : / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / 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 / 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 / cellular response to cadmium ion / ERK1 and ERK2 cascade / cellular response to amino acid starvation / myelination / dendrite cytoplasm / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / caveola / positive regulation of translation / long-term synaptic potentiation / animal organ morphogenesis Similarity search - Function | ||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Kummer, L. / Mittl, P.R. / Pluckthun, A. | ||||||
![]() | ![]() Title: Structural and Functional Analysis of Phosphorylation-Specific Binders of the Kinase Erk from Designed Ankyrin Repeat Protein Libraries. Authors: Kummer, L. / Parizek, P. / Rube, P. / Millgramm, B. / Prinz, A. / Mittl, P.R. / Kaufholz, M. / Zimmermann, B. / Herberg, F.W. / Pluckthun, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.3 KB | Display | ![]() |
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PDB format | ![]() | 169.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zuvC ![]() 1erk ![]() 1mj0S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42230.508 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P63086, mitogen-activated protein kinase |
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#2: Protein | Mass: 18328.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PDST67_E40 / Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.6 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 100 MM TRIS-HOAC (PH 8.5), 20% PEG4K, 5 MM CDCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 12, 2010 / Details: ELECTRON OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→5.41 Å / Num. obs: 42412 / % possible obs: 82.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.21 |
Reflection shell | Resolution: 1.87→1.88 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.3 / % possible all: 44.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1ERK, 1MJ0 Resolution: 1.97→19.43 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.11 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A 175 - A 179 LIE IN A REGION OF WEAK ELECTRON DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.705 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→19.43 Å
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Refine LS restraints |
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