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- PDB-2lb2: Structure of the second domain of human Nedd4L in complex with a ... -
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Basic information
Entry | Database: PDB / ID: 2lb2 | ||||||
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Title | Structure of the second domain of human Nedd4L in complex with a phosphorylated pTPY motif derived from human Smad3 | ||||||
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![]() | SIGNALING PROTEIN/TRANSCRIPTION / Nedd4L / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION complex | ||||||
Function / homology | ![]() nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / transdifferentiation / sterol response element binding / paraxial mesoderm morphogenesis / positive regulation of caveolin-mediated endocytosis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / transdifferentiation / sterol response element binding / paraxial mesoderm morphogenesis / positive regulation of caveolin-mediated endocytosis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / nodal signaling pathway / regulation of striated muscle tissue development / SMAD protein complex / negative regulation of potassium ion transmembrane transporter activity / immune system development / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / RUNX3 regulates BCL2L11 (BIM) transcription / DEAD/H-box RNA helicase binding / bHLH transcription factor binding / pericardium development / regulation of sodium ion transmembrane transport / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of sodium ion transmembrane transporter activity / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / negative regulation of protein localization to cell surface / regulation of transforming growth factor beta receptor signaling pathway / regulation of membrane repolarization / embryonic foregut morphogenesis / negative regulation of wound healing / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / regulation of membrane depolarization / primary miRNA processing / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / nuclear glucocorticoid receptor binding / endoderm development / positive regulation of dendrite extension / Formation of definitive endoderm / embryonic pattern specification / signal transduction involved in regulation of gene expression / activin receptor signaling pathway / Signaling by Activin / SMAD protein signal transduction / ventricular cardiac muscle cell action potential / potassium channel inhibitor activity / Formation of axial mesoderm / HECT-type E3 ubiquitin transferase / cell-cell junction organization / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / I-SMAD binding / sodium channel inhibitor activity / Interleukin-37 signaling / response to angiotensin / regulation of monoatomic ion transmembrane transport / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of cardiac muscle hypertrophy in response to stress / nuclear inner membrane / RUNX3 regulates CDKN1A transcription / ureteric bud development / DNA-binding transcription repressor activity / adrenal gland development / regulation of dendrite morphogenesis / negative regulation of fat cell differentiation / negative regulation of cytosolic calcium ion concentration / heart looping / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / R-SMAD binding / positive regulation of focal adhesion assembly / thyroid gland development / mesoderm formation / regulation of immune response / developmental growth / potassium channel regulator activity / sodium channel regulator activity / phosphatase binding / anatomical structure morphogenesis / negative regulation of osteoblast differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cis-regulatory region sequence-specific DNA binding / protein K48-linked ubiquitination / positive regulation of bone mineralization / somitogenesis / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Macias, M.J. / Aragon, E. / Goerner, N. / Zaromytidou, A. / Xi, Q. / Escobedo, A. / Massague, J. | ||||||
![]() | ![]() Title: A Smad action turnover switch operated by WW domain readers of a phosphoserine code. Authors: Aragon, E. / Goerner, N. / Zaromytidou, A.I. / Xi, Q. / Escobedo, A. / Massague, J. / Macias, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365.2 KB | Display | ![]() |
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PDB format | ![]() | 316.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 632.2 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 44.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lajC ![]() 2lawC ![]() 2laxC ![]() 2layC ![]() 2lazC ![]() 2lb0C ![]() 2lb1C ![]() 2lb3C C: citing same article ( |
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Similar structure data | |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 4184.675 Da / Num. of mol.: 1 / Fragment: residues 386-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 1341.272 Da / Num. of mol.: 1 / Fragment: residues 178-189 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Structure of the second domain of human Nedd4L in complex with a doubly phosphorylated human Smad3 (res 178-189) derived peptide. | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 0.420 / pH: 7 / Pressure: ambient / Temperature: 285 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 766 / NOE intraresidue total count: 0 / NOE long range total count: 298 / NOE medium range total count: 47 / NOE sequential total count: 249 / Hydrogen bond constraints total count: 10 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 300 / Conformers submitted total number: 25 |