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Open data
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Basic information
Entry | Database: PDB / ID: 5n7g | ||||||
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Title | MAGI-1 complexed with a synthetic pRSK1 peptide | ||||||
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![]() | SIGNALING PROTEIN / docking / signaling / complex | ||||||
Function / homology | ![]() regulation of translation in response to stress / positive regulation of low-density lipoprotein particle receptor binding / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / ribosomal protein S6 kinase activity ...regulation of translation in response to stress / positive regulation of low-density lipoprotein particle receptor binding / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of hepatic stellate cell activation / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / positive regulation of cell-cell adhesion / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / Gastrin-CREB signalling pathway via PKC and MAPK / osteoclast development / calcium-dependent phospholipid binding / negative regulation of receptor internalization / RSK activation / collagen fibril organization / negative regulation of TOR signaling / Dissolution of Fibrin Clot / S100 protein binding / vesicle membrane / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / ERK/MAPK targets / alpha-actinin binding / positive regulation of exocytosis / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / regulation of neurogenesis / basement membrane / Transcriptional and post-translational regulation of MITF-M expression and activity / Smooth Muscle Contraction / bicellular tight junction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to activity / cell projection / cell periphery / positive regulation of cell differentiation / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / cell-cell junction / melanosome / cell junction / late endosome membrane / midbody / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / protein-containing complex assembly / protease binding / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / vesicle / early endosome / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / cell adhesion / intracellular signal transduction / endosome / lysosomal membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / calcium ion binding / Neutrophil degranulation / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gogl, G. / Nyitray, L. | ||||||
![]() | ![]() Title: Dynamic control of RSK complexes by phosphoswitch-based regulation. Authors: Gogl, G. / Biri-Kovacs, B. / Poti, A.L. / Vadaszi, H. / Szeder, B. / Bodor, A. / Schlosser, G. / Acs, A. / Turiak, L. / Buday, L. / Alexa, A. / Nyitray, L. / Remenyi, 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 | ![]() | 307.9 KB | Display | ![]() |
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PDB format | ![]() | 250.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5n7dC ![]() 5n7fC ![]() 1xjlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48099.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MAGI1, AIP3, BAIAP1, BAP1, TNRC19, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D Production host: ![]() ![]() #2: Protein/peptide | | Mass: 839.890 Da / Num. of mol.: 1 / Fragment: UNP residues 88-94 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: Q15418, non-specific serine/threonine protein kinase #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 14% PEG 8000, 200 mM MgCl2, 100 mM TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→49.105 Å / Num. obs: 24379 / % possible obs: 99.9 % / Redundancy: 6.86 % / Rrim(I) all: 0.268 / Net I/σ(I): 8.36 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.49 / Num. unique all: 1785 / Rrim(I) all: 0.897 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1xjl Resolution: 2.95→49.105 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→49.105 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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